Updates to website
This commit is contained in:
clairblacketer
parent
38625309ff
commit
6395f213ba
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@ -1,5 +1,6 @@
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# Generated by roxygen2: do not edit by hand
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# Generated by roxygen2: do not edit by hand
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export(createDdlFromFile)
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export(downloadCurrentDdl)
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export(downloadCurrentDdl)
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export(parseWiki)
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export(parseWiki)
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export(writeConstraints)
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export(writeConstraints)
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@ -0,0 +1,70 @@
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# Copyright 2019 Observational Health Data Sciences and Informatics
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#
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# This file is part of DDLGeneratr
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#' Create a DDL script from a two csv files that detail the OMOP CDM Specifications. These files also form the basis of the CDM documentation and the Data Quality
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#' Dashboard.
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#'
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#' @param cdmTableCsvLoc The location of the csv file with the high-level CDM table information. This is defaulted to "inst/csv/OMOP_CDMv5.3.1_Table_Level.csv".
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#' If a new version of this file was committed to the CDM repository the package automatically will grab it and place it in "inst/csv/".
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#' @param cdmVersion The location of the csv file with the CDM field information. This is defaulted to "inst/csv/OMOP_CDMv5.3.1_Field_Level.csv".
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#' If a new version of this file was committed to the CDM repository the package automatically will grab it and place it in "inst/csv/".
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#' @export
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createDdlFromFile <- function(cdmTableCsvLoc = "inst/csv/OMOP_CDMv5.3.1_Table_Level.csv",
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cdmFieldCsvLoc = "inst/csv/OMOP_CDMv5.3.1_Field_Level.csv"){
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tableSpecs <- read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)
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cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
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tableList <- tableSpecs$cdmTableName
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s <- c()
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for (t in tableList){
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table <- subset(cdmSpecs, cdmTableName == t)
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fields <- table$cdmFieldName
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if ('person_id' %in% fields){
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q <- "--HINT DISTRIBUTE ON KEY (person_id)"
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} else {
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q <- "--HINT DISTRIBUTE ON RANDOM"
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}
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s <- c(s, q, paste0("CREATE TABLE ", t, " ("))
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end <- length(fields)
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a <- c()
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for(f in fields) {
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if (subset(table, cdmFieldName == f, isRequired) == "Yes") {
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r <- (" NOT NULL")
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} else {
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r <- (" NULL")
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}
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if (f == fields[[end]]) {
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e <- (" );")
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} else {
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e <- (",")
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}
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a <- c(a, paste0(f," ",subset(table, cdmFieldName == f, cdmDatatype),r,e))
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}
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s <- c(s, a, "")
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}
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return(s)
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}
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@ -1,4 +1,4 @@
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# Copyright 2017 Observational Health Data Sciences and Informatics
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# Copyright 2019 Observational Health Data Sciences and Informatics
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#
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#
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# This file is part of DDLGeneratr
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# This file is part of DDLGeneratr
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#
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#
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@ -384,6 +384,13 @@ div.tocify {
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</a>
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</a>
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</li>
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</li>
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<li>
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<a href="background.html">
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<span class="fa fa-landmark"></span>
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Background
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</a>
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</li>
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<li>
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<li>
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<a href="dataModelConventions.html">
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<a href="dataModelConventions.html">
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<span class="fa fa-list-alt"></span>
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<span class="fa fa-list-alt"></span>
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@ -408,6 +415,34 @@ div.tocify {
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</li>
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</li>
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</ul>
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</ul>
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</li>
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</li>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<span class="fa fa-plus-square"></span>
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Proposals
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="reviewProposals.html">Under Review</a>
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</li>
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<li class="dropdown-submenu">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="https://github.com/OHDSI/CommonDataModel/files/2642492/Oncology.CDM.Proposal.2018-12-02.pdf">Oncology CDM Proposal</a>
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</li>
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<li>
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<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
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</li>
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<li>
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<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<li>
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<a href="faq.html">
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<a href="faq.html">
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<span class="fa fa-question"></span>
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<span class="fa fa-question"></span>
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|
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@ -424,7 +459,12 @@ div.tocify {
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</li>
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</li>
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</ul>
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</ul>
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<ul class="nav navbar-nav navbar-right">
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<ul class="nav navbar-nav navbar-right">
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|
<li>
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|
<a href="https://github.com/OHDSI/CommonDataModel">
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<span class="fa fa-github fa-lg"></span>
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</a>
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</li>
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</ul>
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</ul>
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</div><!--/.nav-collapse -->
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</div><!--/.nav-collapse -->
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</div><!--/.container -->
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</div><!--/.container -->
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@ -0,0 +1,553 @@
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<!DOCTYPE html>
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<html xmlns="http://www.w3.org/1999/xhtml">
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<head>
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<meta charset="utf-8" />
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<meta name="generator" content="pandoc" />
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|
||||||
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<title>background.utf8</title>
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<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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||||||
|
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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||||||
|
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
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||||||
|
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
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||||||
|
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
|
||||||
|
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
|
||||||
|
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
|
||||||
|
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
|
||||||
|
<script src="site_libs/navigation-1.1/tabsets.js"></script>
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||||||
|
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
|
||||||
|
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
|
||||||
|
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
|
||||||
|
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
|
||||||
|
<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
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||||||
|
<style type="text/css">code{white-space: pre;}</style>
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<style type="text/css">
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|
pre:not([class]) {
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|
background-color: white;
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|
}
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</style>
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<script type="text/javascript">
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|
if (window.hljs) {
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||||||
|
hljs.configure({languages: []});
|
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|
hljs.initHighlightingOnLoad();
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||||||
|
if (document.readyState && document.readyState === "complete") {
|
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|
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
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||||||
|
}
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}
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||||||
|
</script>
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||||||
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|
<style type="text/css">
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||||||
|
h1 {
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|
font-size: 34px;
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}
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||||||
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h1.title {
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|
font-size: 38px;
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}
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h2 {
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|
font-size: 30px;
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}
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h3 {
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font-size: 24px;
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}
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h4 {
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font-size: 18px;
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}
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h5 {
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font-size: 16px;
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}
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h6 {
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font-size: 12px;
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}
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.table th:not([align]) {
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text-align: left;
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|
}
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</style>
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|
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|
<link rel="stylesheet" href="style.css" type="text/css" />
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||||||
|
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||||||
|
</head>
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|
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||||||
|
<body>
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|
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|
<style type = "text/css">
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|
.main-container {
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|
max-width: 940px;
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|
margin-left: auto;
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||||||
|
margin-right: auto;
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||||||
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}
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|
code {
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|
color: inherit;
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|
background-color: rgba(0, 0, 0, 0.04);
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|
}
|
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|
img {
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||||||
|
max-width:100%;
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|
height: auto;
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}
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|
.tabbed-pane {
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padding-top: 12px;
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}
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||||||
|
.html-widget {
|
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|
margin-bottom: 20px;
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|
}
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button.code-folding-btn:focus {
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|
outline: none;
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|
}
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summary {
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||||||
|
display: list-item;
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}
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</style>
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<style type="text/css">
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/* padding for bootstrap navbar */
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body {
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|
padding-top: 51px;
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|
padding-bottom: 40px;
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|
}
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/* offset scroll position for anchor links (for fixed navbar) */
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.section h1 {
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padding-top: 56px;
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margin-top: -56px;
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}
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.section h2 {
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padding-top: 56px;
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margin-top: -56px;
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}
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.section h3 {
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padding-top: 56px;
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margin-top: -56px;
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}
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.section h4 {
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padding-top: 56px;
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margin-top: -56px;
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|
}
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.section h5 {
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|
padding-top: 56px;
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margin-top: -56px;
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||||||
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}
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|
.section h6 {
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|
padding-top: 56px;
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||||||
|
margin-top: -56px;
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||||||
|
}
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||||||
|
.dropdown-submenu {
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||||||
|
position: relative;
|
||||||
|
}
|
||||||
|
.dropdown-submenu>.dropdown-menu {
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||||||
|
top: 0;
|
||||||
|
left: 100%;
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||||||
|
margin-top: -6px;
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||||||
|
margin-left: -1px;
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||||||
|
border-radius: 0 6px 6px 6px;
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||||||
|
}
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||||||
|
.dropdown-submenu:hover>.dropdown-menu {
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||||||
|
display: block;
|
||||||
|
}
|
||||||
|
.dropdown-submenu>a:after {
|
||||||
|
display: block;
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||||||
|
content: " ";
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||||||
|
float: right;
|
||||||
|
width: 0;
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||||||
|
height: 0;
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||||||
|
border-color: transparent;
|
||||||
|
border-style: solid;
|
||||||
|
border-width: 5px 0 5px 5px;
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||||||
|
border-left-color: #cccccc;
|
||||||
|
margin-top: 5px;
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||||||
|
margin-right: -10px;
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||||||
|
}
|
||||||
|
.dropdown-submenu:hover>a:after {
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||||||
|
border-left-color: #ffffff;
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||||||
|
}
|
||||||
|
.dropdown-submenu.pull-left {
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||||||
|
float: none;
|
||||||
|
}
|
||||||
|
.dropdown-submenu.pull-left>.dropdown-menu {
|
||||||
|
left: -100%;
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||||||
|
margin-left: 10px;
|
||||||
|
border-radius: 6px 0 6px 6px;
|
||||||
|
}
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||||||
|
</style>
|
||||||
|
|
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|
<script>
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||||||
|
// manage active state of menu based on current page
|
||||||
|
$(document).ready(function () {
|
||||||
|
// active menu anchor
|
||||||
|
href = window.location.pathname
|
||||||
|
href = href.substr(href.lastIndexOf('/') + 1)
|
||||||
|
if (href === "")
|
||||||
|
href = "index.html";
|
||||||
|
var menuAnchor = $('a[href="' + href + '"]');
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||||||
|
|
||||||
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// mark it active
|
||||||
|
menuAnchor.parent().addClass('active');
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||||||
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||||||
|
// if it's got a parent navbar menu mark it active as well
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||||||
|
menuAnchor.closest('li.dropdown').addClass('active');
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||||||
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});
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</script>
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||||||
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<div class="container-fluid main-container">
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||||||
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||||||
|
<!-- tabsets -->
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||||||
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|
||||||
|
<style type="text/css">
|
||||||
|
.tabset-dropdown > .nav-tabs {
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||||||
|
display: inline-table;
|
||||||
|
max-height: 500px;
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||||||
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min-height: 44px;
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||||||
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overflow-y: auto;
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||||||
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background: white;
|
||||||
|
border: 1px solid #ddd;
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||||||
|
border-radius: 4px;
|
||||||
|
}
|
||||||
|
|
||||||
|
.tabset-dropdown > .nav-tabs > li.active:before {
|
||||||
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content: "";
|
||||||
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font-family: 'Glyphicons Halflings';
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||||||
|
display: inline-block;
|
||||||
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padding: 10px;
|
||||||
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border-right: 1px solid #ddd;
|
||||||
|
}
|
||||||
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|
||||||
|
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
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||||||
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content: "";
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||||||
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border: none;
|
||||||
|
}
|
||||||
|
|
||||||
|
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||||
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content: "";
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||||||
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font-family: 'Glyphicons Halflings';
|
||||||
|
display: inline-block;
|
||||||
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padding: 10px;
|
||||||
|
border-right: 1px solid #ddd;
|
||||||
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}
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||||||
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||||||
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.tabset-dropdown > .nav-tabs > li.active {
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||||||
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display: block;
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||||||
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}
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||||||
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||||||
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.tabset-dropdown > .nav-tabs > li > a,
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<a class="navbar-brand" href="index.html"><div><img src="ohdsi16x16.png"></img> OMOP Common Data Model </div></a>
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Conventions
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CDM Versions
|
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<span class="caret"></span>
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</a>
|
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|
<ul class="dropdown-menu" role="menu">
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<a href="cdm531.html">CDM v5.3.1</a>
|
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|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="cdm60.html">CDM v6.0</a>
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Proposals
|
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<span class="caret"></span>
|
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</a>
|
||||||
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<ul class="dropdown-menu" role="menu">
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<li class="dropdown-submenu">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
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<ul class="dropdown-menu" role="menu">
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/files/2642492/Oncology.CDM.Proposal.2018-12-02.pdf">Oncology CDM Proposal</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</li>
|
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|
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|
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|
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<a href="faq.html">
|
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<span class="fa fa-question"></span>
|
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FAQ
|
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|
</a>
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|
||||||
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<li>
|
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|
<a href="contribute.html">
|
||||||
|
<span class="fa fa-wrench"></span>
|
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|
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Contribute
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|
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</ul>
|
||||||
|
<ul class="nav navbar-nav navbar-right">
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<a href="https://github.com/OHDSI/CommonDataModel">
|
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<span class="fa fa-github fa-lg"></span>
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
</div><!--/.navbar -->
|
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|
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|
<div class="fluid-row" id="header">
|
||||||
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|
||||||
|
|
||||||
|
|
||||||
|
<h1 class="title toc-ignore"><div>
|
||||||
|
<img src="ohdsi40x40.png"></img> OMOP CDM Background
|
||||||
|
</div></h1>
|
||||||
|
|
||||||
|
</div>
|
||||||
|
|
||||||
|
|
||||||
|
<div id="background" class="section level2">
|
||||||
|
<h2>Background</h2>
|
||||||
|
<p>The Observational Medical Outcomes Partnership (OMOP) was a public-private partnership established to inform the appropriate use of observational healthcare databases for studying the effects of medical products. Over the course of the 5-year project and through its community of researchers from industry, government, and academia, OMOP successfully achieved its aims to:</p>
|
||||||
|
<ul>
|
||||||
|
<li>Conduct methodological research to empirically evaluate the performance of various analytical methods on their ability to identify true associations and avoid false findings</li>
|
||||||
|
<li>Develop tools and capabilities for transforming, characterizing, and analysing disparate data sources across the health care delivery spectrum</li>
|
||||||
|
<li>Establish a shared resource so that the broader research community can collaboratively advance the science</li>
|
||||||
|
</ul>
|
||||||
|
<p>The results of OMOP’s research has been widely published and presented at scientific conferences, including <a href="https://www.ohdsi.org/events/2019-ohdsi-symposium/">annual symposia</a>.</p>
|
||||||
|
<p>The OMOP Legacy continues…</p>
|
||||||
|
<p>The community is actively using the OMOP Common Data Model for their various research purposes. Those tools will continue to be maintained and supported, and information about this work is available in the <a href="http://www.github.com/ohdsi">public domain</a>.</p>
|
||||||
|
<p>The OMOP Common Data Model will continue to be an open-source community standard for observational healthcare data. The model specifications and associated work products will be placed in the public domain, and the entire research community is encouraged to use these tools to support everybody’s own research activities.</p>
|
||||||
|
</div>
|
||||||
|
<div id="the-role-of-the-common-data-model" class="section level2">
|
||||||
|
<h2>The Role of the Common Data Model</h2>
|
||||||
|
<p>No single observational data source provides a comprehensive view of the clinical data a patient accumulates while receiving healthcare, and therefore none can be sufficient to meet all expected outcome analysis needs. This explains the need for assessing and analyzing multiple data sources concurrently using a common data standard. This standard is provided by the OMOP Common Data Model (CDM).</p>
|
||||||
|
<p>The CDM is designed to support the conduct of research to identify and evaluate associations between interventions (drug exposure, procedures, healthcare policy changes etc.) and outcomes caused by these interventions (condition occurrences, procedures, drug exposure etc.). Outcomes can be efficacious (benefit) or adverse (safety risk). Often times, specific patient cohorts (e.g., those taking a certain drug or suffering from a certain disease) may be defined for treatments or outcomes, using clinical events (diagnoses, observations, procedures, etc.) that occur in predefined temporal relationships to each other. The CDM, combined with its standardized content (via the Standardized Vocabularies), will ensure that research methods can be systematically applied to produce meaningfully comparable and reproducible results.</p>
|
||||||
|
</div>
|
||||||
|
<div id="design-principles" class="section level2">
|
||||||
|
<h2>Design Principles</h2>
|
||||||
|
<p>The CDM is designed to include all observational health data elements (experiences of the patient receiving health care) that are relevant for analytic use cases to support the generation of reliable scientific evidence about disease natural history, healthcare delivery, effects of medical interventions, the identification of demographic information, health care interventions and outcomes.</p>
|
||||||
|
<p>Therefore, the CDM is designed to store observational data to allow for research, under the following principles:</p>
|
||||||
|
<ul>
|
||||||
|
<li><strong>Suitability for purpose:</strong> The CDM aims to provide data organized in a way optimal for analysis, rather than for the purpose of addressing the operational needs of health care providers or payers.</li>
|
||||||
|
<li><strong>Data protection:</strong> All data that might jeopardize the identity and protection of patients, such as names, precise birthdays etc. are limited. Exceptions are possible where the research expressly requires more detailed information, such as precise birth dates for the study of infants.</li>
|
||||||
|
<li><strong>Design of domains:</strong> The domains are modeled in a person-centric relational data model, where for each record the identity of the person and a date is captured as a minimum.</li>
|
||||||
|
<li><strong>Rationale for domains:</strong> Domains are identified and separately defined in an entity-relationship model if they have an analysis use case and the domain has specific attributes that are not otherwise applicable. All other data can be preserved as an observation in an entity-attribute-value structure.</li>
|
||||||
|
<li><strong>Standardized Vocabularies:</strong> To standardize the content of those records, the CDM relies on the Standardized Vocabularies containing all necessary and appropriate corresponding standard healthcare concepts.</li>
|
||||||
|
<li><strong>Reuse of existing vocabularies:</strong> If possible, these concepts are leveraged from national or industry standardization or vocabulary definition organizations or initiatives, such as the National Library of Medicine, the Department of Veterans’ Affairs, the Center of Disease Control and Prevention, etc.</li>
|
||||||
|
<li><strong>Maintaining source codes:</strong> Even though all codes are mapped to the Standardized Vocabularies, the model also stores the original source code to ensure no information is lost.</li>
|
||||||
|
<li><strong>Technology neutrality:</strong> The CDM does not require a specific technology. It can be realized in any relational database, such as Oracle, SQL Server etc., or as SAS analytical datasets.</li>
|
||||||
|
<li><strong>Scalability:</strong> The CDM is optimized for data processing and computational analysis to accommodate data sources that vary in size, including databases with up to hundreds of millions of persons and billions of clinical observations.</li>
|
||||||
|
<li><strong>Backwards compatibility:</strong> All changes from previous CDMs are clearly delineated in the <a href="https://github.com/OHDSI/CommonDataModel">github repository</a>. Older versions of the CDM can be easily created from the CDMv5, and no information is lost that was present previously.</li>
|
||||||
|
</ul>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
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|
||||||
|
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|
||||||
|
|
||||||
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|
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|
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|
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|
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|
||||||
|
|
||||||
|
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|
||||||
|
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|
||||||
|
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|
||||||
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|
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|
||||||
<a href="dataModelConventions.html">
|
<a href="dataModelConventions.html">
|
||||||
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|
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|
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|
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|
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|
||||||
|
|
||||||
|
Proposals
|
||||||
|
|
||||||
|
<span class="caret"></span>
|
||||||
|
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|
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|
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|
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|
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|
||||||
|
<a href="reviewProposals.html">Under Review</a>
|
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|
||||||
|
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|
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|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
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|
<ul class="dropdown-menu" role="menu">
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/files/2642492/Oncology.CDM.Proposal.2018-12-02.pdf">Oncology CDM Proposal</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||||
|
</li>
|
||||||
|
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|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||||
|
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|
||||||
|
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|
||||||
|
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|
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|
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|
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|
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|
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<a href="faq.html">
|
<a href="faq.html">
|
||||||
<span class="fa fa-question"></span>
|
<span class="fa fa-question"></span>
|
||||||
|
|
@ -426,7 +461,12 @@ div.tocify {
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
<ul class="nav navbar-nav navbar-right">
|
<ul class="nav navbar-nav navbar-right">
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||||
|
<span class="fa fa-github fa-lg"></span>
|
||||||
|
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</div><!--/.nav-collapse -->
|
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|
||||||
</div><!--/.container -->
|
</div><!--/.container -->
|
||||||
|
|
@ -441,32 +481,13 @@ div.tocify {
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|
||||||
<p>##TODO for CDM # File bug reports</p>
|
<div id="file-bug-reports" class="section level1">
|
||||||
<p>If you’ve found a bug you can help out by filing a bug report. Each package has an issue tracker where you can create a new issue. Try and be as specific as possible. What error message occurs? Can you provide a simple example to reproduce the problem? What versions of the various packages are you running?</p>
|
<h1>File bug reports</h1>
|
||||||
<div id="write-help-files" class="section level1">
|
<p>If you’ve found a bug you can help out by filing a bug report. Try and be as specific as possible. What error message occurs? Can you provide a simple example to reproduce the problem? What versions of the various packages are you running?</p>
|
||||||
<h1>Write help files</h1>
|
|
||||||
<p>If you’re a bit more experienced with the Methods Library and are looking to improve your open source development skills, the next step up is to contribute a pull request to a Methods Library package. The most important thing to know is that Methods Library packages use <a href="https://github.com/klutometis/roxygen">roxygen2</a>: this means that documentation is found in the R code close to the source of each function.</p>
|
|
||||||
</div>
|
</div>
|
||||||
<div id="write-unit-tests" class="section level1">
|
<div id="join-meetings" class="section level1">
|
||||||
<h1>Write unit tests</h1>
|
<h1>Join meetings</h1>
|
||||||
<p>An important part of validating the methods in the library is unit testing. A unit test is a small program that tests a specific function in the library. For example, there are <a href="https://github.com/OHDSI/CohortMethod/blob/master/tests/testthat/test-psFunctions.R#L5">several unit tests</a> that make sure the propensity score matching works correctly. We can never have enough unit tests, and writing unit tests is an excellent way to learn how the Methods Library packages work under the hood.</p>
|
<p>Please come to meetings and contribute to the discussion! All details can be found our home page.</p>
|
||||||
</div>
|
|
||||||
<div id="add-methods" class="section level1">
|
|
||||||
<h1>Add methods</h1>
|
|
||||||
<p>We are always looking for new methods and packages to add to the Methods Libary. However, in order to qualify for inclusion a package must meet the following requirements:</p>
|
|
||||||
<ul>
|
|
||||||
<li>Pass R check without warnings or notes.</li>
|
|
||||||
<li>Adhere to <a href="https://ohdsi.github.io/MethodsLibrary/contribute.html#code_style_guidelines">OHDSI’s code style guidelines</a> and overall development practices.</li>
|
|
||||||
<li>Have <a href="http://www.ohdsi.org/web/wiki/doku.php?id=development:unit_testing_in_r">unit tests</a> that test the package’s most important routines.</li>
|
|
||||||
<li>For population-level estimation methods: be evaluated using the OHDSI Methods Benchmark.</li>
|
|
||||||
</ul>
|
|
||||||
</div>
|
|
||||||
<div id="code-style-guidelines" class="section level1">
|
|
||||||
<h1>Code style guidelines</h1>
|
|
||||||
<ul>
|
|
||||||
<li><a href="http://www.ohdsi.org/web/wiki/doku.php?id=development:ohdsi_code_style_for_r">Style guide for R code</a></li>
|
|
||||||
<li><a href="http://www.ohdsi.org/web/wiki/doku.php?id=development:ohdsi_code_style_for_sql">Style guide for SQL code</a></li>
|
|
||||||
</ul>
|
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -386,6 +386,13 @@ div.tocify {
|
||||||
|
|
||||||
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|
</a>
|
||||||
</li>
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="background.html">
|
||||||
|
<span class="fa fa-landmark"></span>
|
||||||
|
|
||||||
|
Background
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="dataModelConventions.html">
|
<a href="dataModelConventions.html">
|
||||||
<span class="fa fa-list-alt"></span>
|
<span class="fa fa-list-alt"></span>
|
||||||
|
|
@ -410,6 +417,34 @@ div.tocify {
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</li>
|
</li>
|
||||||
|
<li class="dropdown">
|
||||||
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
|
<span class="fa fa-plus-square"></span>
|
||||||
|
|
||||||
|
Proposals
|
||||||
|
|
||||||
|
<span class="caret"></span>
|
||||||
|
</a>
|
||||||
|
<ul class="dropdown-menu" role="menu">
|
||||||
|
<li>
|
||||||
|
<a href="reviewProposals.html">Under Review</a>
|
||||||
|
</li>
|
||||||
|
<li class="dropdown-submenu">
|
||||||
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||||
|
<ul class="dropdown-menu" role="menu">
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/files/2642492/Oncology.CDM.Proposal.2018-12-02.pdf">Oncology CDM Proposal</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="faq.html">
|
<a href="faq.html">
|
||||||
<span class="fa fa-question"></span>
|
<span class="fa fa-question"></span>
|
||||||
|
|
@ -426,7 +461,12 @@ div.tocify {
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
<ul class="nav navbar-nav navbar-right">
|
<ul class="nav navbar-nav navbar-right">
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||||
|
<span class="fa fa-github fa-lg"></span>
|
||||||
|
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</div><!--/.nav-collapse -->
|
</div><!--/.nav-collapse -->
|
||||||
</div><!--/.container -->
|
</div><!--/.container -->
|
||||||
|
|
|
||||||
|
|
@ -288,6 +288,13 @@ $(document).ready(function () {
|
||||||
|
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="background.html">
|
||||||
|
<span class="fa fa-landmark"></span>
|
||||||
|
|
||||||
|
Background
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="dataModelConventions.html">
|
<a href="dataModelConventions.html">
|
||||||
<span class="fa fa-list-alt"></span>
|
<span class="fa fa-list-alt"></span>
|
||||||
|
|
@ -312,6 +319,34 @@ $(document).ready(function () {
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</li>
|
</li>
|
||||||
|
<li class="dropdown">
|
||||||
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
|
<span class="fa fa-plus-square"></span>
|
||||||
|
|
||||||
|
Proposals
|
||||||
|
|
||||||
|
<span class="caret"></span>
|
||||||
|
</a>
|
||||||
|
<ul class="dropdown-menu" role="menu">
|
||||||
|
<li>
|
||||||
|
<a href="reviewProposals.html">Under Review</a>
|
||||||
|
</li>
|
||||||
|
<li class="dropdown-submenu">
|
||||||
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||||
|
<ul class="dropdown-menu" role="menu">
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/files/2642492/Oncology.CDM.Proposal.2018-12-02.pdf">Oncology CDM Proposal</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="faq.html">
|
<a href="faq.html">
|
||||||
<span class="fa fa-question"></span>
|
<span class="fa fa-question"></span>
|
||||||
|
|
@ -328,7 +363,12 @@ $(document).ready(function () {
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
<ul class="nav navbar-nav navbar-right">
|
<ul class="nav navbar-nav navbar-right">
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||||
|
<span class="fa fa-github fa-lg"></span>
|
||||||
|
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</div><!--/.nav-collapse -->
|
</div><!--/.nav-collapse -->
|
||||||
</div><!--/.container -->
|
</div><!--/.container -->
|
||||||
|
|
|
||||||
193
docs/index.html
193
docs/index.html
|
|
@ -19,9 +19,6 @@
|
||||||
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
|
<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/html5shiv.min.js"></script>
|
||||||
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
|
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
|
||||||
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
|
|
||||||
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
|
|
||||||
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
|
|
||||||
<script src="site_libs/navigation-1.1/tabsets.js"></script>
|
<script src="site_libs/navigation-1.1/tabsets.js"></script>
|
||||||
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
|
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
|
||||||
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
|
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
|
||||||
|
|
@ -271,101 +268,6 @@ $(document).ready(function () {
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
<script>
|
|
||||||
$(document).ready(function () {
|
|
||||||
|
|
||||||
// move toc-ignore selectors from section div to header
|
|
||||||
$('div.section.toc-ignore')
|
|
||||||
.removeClass('toc-ignore')
|
|
||||||
.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
|
|
||||||
|
|
||||||
// establish options
|
|
||||||
var options = {
|
|
||||||
selectors: "h1,h2,h3",
|
|
||||||
theme: "bootstrap3",
|
|
||||||
context: '.toc-content',
|
|
||||||
hashGenerator: function (text) {
|
|
||||||
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
|
|
||||||
},
|
|
||||||
ignoreSelector: ".toc-ignore",
|
|
||||||
scrollTo: 0
|
|
||||||
};
|
|
||||||
options.showAndHide = true;
|
|
||||||
options.smoothScroll = true;
|
|
||||||
|
|
||||||
// tocify
|
|
||||||
var toc = $("#TOC").tocify(options).data("toc-tocify");
|
|
||||||
});
|
|
||||||
</script>
|
|
||||||
|
|
||||||
<style type="text/css">
|
|
||||||
|
|
||||||
#TOC {
|
|
||||||
margin: 25px 0px 20px 0px;
|
|
||||||
}
|
|
||||||
@media (max-width: 768px) {
|
|
||||||
#TOC {
|
|
||||||
position: relative;
|
|
||||||
width: 100%;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
.toc-content {
|
|
||||||
padding-left: 30px;
|
|
||||||
padding-right: 40px;
|
|
||||||
}
|
|
||||||
|
|
||||||
div.main-container {
|
|
||||||
max-width: 1200px;
|
|
||||||
}
|
|
||||||
|
|
||||||
div.tocify {
|
|
||||||
width: 20%;
|
|
||||||
max-width: 260px;
|
|
||||||
max-height: 85%;
|
|
||||||
}
|
|
||||||
|
|
||||||
@media (min-width: 768px) and (max-width: 991px) {
|
|
||||||
div.tocify {
|
|
||||||
width: 25%;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
@media (max-width: 767px) {
|
|
||||||
div.tocify {
|
|
||||||
width: 100%;
|
|
||||||
max-width: none;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
.tocify ul, .tocify li {
|
|
||||||
line-height: 20px;
|
|
||||||
}
|
|
||||||
|
|
||||||
.tocify-subheader .tocify-item {
|
|
||||||
font-size: 0.90em;
|
|
||||||
padding-left: 25px;
|
|
||||||
text-indent: 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
.tocify .list-group-item {
|
|
||||||
border-radius: 0px;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
</style>
|
|
||||||
|
|
||||||
<!-- setup 3col/9col grid for toc_float and main content -->
|
|
||||||
<div class="row-fluid">
|
|
||||||
<div class="col-xs-12 col-sm-4 col-md-3">
|
|
||||||
<div id="TOC" class="tocify">
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||||
|
|
@ -386,6 +288,13 @@ div.tocify {
|
||||||
|
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="background.html">
|
||||||
|
<span class="fa fa-landmark"></span>
|
||||||
|
|
||||||
|
Background
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="dataModelConventions.html">
|
<a href="dataModelConventions.html">
|
||||||
<span class="fa fa-list-alt"></span>
|
<span class="fa fa-list-alt"></span>
|
||||||
|
|
@ -410,6 +319,34 @@ div.tocify {
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</li>
|
</li>
|
||||||
|
<li class="dropdown">
|
||||||
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
|
<span class="fa fa-plus-square"></span>
|
||||||
|
|
||||||
|
Proposals
|
||||||
|
|
||||||
|
<span class="caret"></span>
|
||||||
|
</a>
|
||||||
|
<ul class="dropdown-menu" role="menu">
|
||||||
|
<li>
|
||||||
|
<a href="reviewProposals.html">Under Review</a>
|
||||||
|
</li>
|
||||||
|
<li class="dropdown-submenu">
|
||||||
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||||
|
<ul class="dropdown-menu" role="menu">
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/files/2642492/Oncology.CDM.Proposal.2018-12-02.pdf">Oncology CDM Proposal</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="faq.html">
|
<a href="faq.html">
|
||||||
<span class="fa fa-question"></span>
|
<span class="fa fa-question"></span>
|
||||||
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|
<ul class="nav navbar-nav navbar-right">
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||||
|
<span class="fa fa-github fa-lg"></span>
|
||||||
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|
||||||
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||||||
<div id="background" class="section level2">
|
<p>The OMOP Common Data Model is managed by the <a href="https://www.ohdsi.org/web/wiki/doku.php?id=projects:workgroups:cdm-wg">OHDSI CDM Working Group</a>. Through the end of 2019 and into 2020 our goal is to fully update the documentation in an effort to facilitate greater understanding of the model. Almost every <a href="https://www.forums.ohdsi.org">forum post</a> relating to a question on how to map data into the CDM inevitably references the technical and difficult-to-understand explanations of the tables and fields currently on the <a href="https://www.github.com/ohdsi/CommonDataModel/wiki">wiki</a>. To remedy this each month we are focusing on one or two tables, diving fully into the user guidance and ETL specifications. We meet twice a month, on the first Tuesday at 1pm est and on the 3rd Tuesday at 9am est (meeting details below).</p>
|
||||||
<h2>Background</h2>
|
<p>In addition to documentation the formal remit of the CDM Working Group is to hear proposals for change, ratifying only those with valid use cases and data to support them. This process will be slower through 2020 though proposals related to existing CDM tables will be considered during the months those tables are being updated. For example November 2019 will be focused on the PERSON and OBSERVATION_PERIOD tables so any proposals related to those two tables will be evaluated during November 2019. Once proposals are accepted they are listed as such and will be integrated in an upcoming version of the OMOP CDM. Currently accepted proposals can be found under the “Proposals” drop down across the top.</p>
|
||||||
<p>The Observational Medical Outcomes Partnership (OMOP) was a public-private partnership established to inform the appropriate use of observational healthcare databases for studying the effects of medical products. Over the course of the 5-year project and through its community of researchers from industry, government, and academia, OMOP successfully achieved its aims to:</p>
|
<div id="cdm-wg-meeting-information" class="section level3">
|
||||||
<ul>
|
<h3>CDM WG Meeting Information</h3>
|
||||||
<li>Conduct methodological research to empirically evaluate the performance of various analytical methods on their ability to identify true associations and avoid false findings</li>
|
<p><strong>Every first Tuesday of the month at 1pm est</strong><br />
|
||||||
<li>Develop tools and capabilities for transforming, characterizing, and analysing disparate data sources across the health care delivery spectrum</li>
|
<a href="https://meet.lync.com/jnj-its/mblacke/V59RPVRY">Skype Meeting</a><br />
|
||||||
<li>Establish a shared resource so that the broader research community can collaboratively advance the science</li>
|
Join by phone<br />
|
||||||
</ul>
|
US toll-free: +1 (908) 316-2436<br />
|
||||||
<p>The results of OMOP’s research has been widely published and presented at scientific conferences, including <a href="https://www.ohdsi.org/events/2019-ohdsi-symposium/">annual symposia</a>.</p>
|
Attendee access code: 215874708#<br />
|
||||||
<p>The OMOP Legacy continues…</p>
|
<a href="https://dialin.lync.com/6071d915-71cb-44a6-ae05-d1830c6bbb14?id=215874708">Global Numbers</a></p>
|
||||||
<p>The community is actively using the OMOP Common Data Model for their various research purposes. Those tools will continue to be maintained and supported, and information about this work is available in the <a href="http://www.github.com/ohdsi">public domain</a>.</p>
|
<p><strong>Every third Tuesday of the month at 9am est</strong><br />
|
||||||
<p>The OMOP Common Data Model will continue to be an open-source community standard for observational healthcare data. The model specifications and associated work products will be placed in the public domain, and the entire research community is encouraged to use these tools to support everybody’s own research activities.</p>
|
<a href="https://meet.lync.com/jnj-its/mblacke/GFMFNJYW">Skype Meeting</a><br />
|
||||||
|
Join by phone<br />
|
||||||
|
US toll-free: +1 (908) 316-2436<br />
|
||||||
|
Attendee access code: 180836323#<br />
|
||||||
|
<a href="https://dialin.lync.com/6071d915-71cb-44a6-ae05-d1830c6bbb14?id=180836323">Global Numbers</a></p>
|
||||||
</div>
|
</div>
|
||||||
<div id="the-role-of-the-common-data-model" class="section level2">
|
<div id="cdm-wg-important-links" class="section level3">
|
||||||
<h2>The Role of the Common Data Model</h2>
|
<h3>CDM WG Important Links</h3>
|
||||||
<p>No single observational data source provides a comprehensive view of the clinical data a patient accumulates while receiving healthcare, and therefore none can be sufficient to meet all expected outcome analysis needs. This explains the need for assessing and analyzing multiple data sources concurrently using a common data standard. This standard is provided by the OMOP Common Data Model (CDM).</p>
|
|
||||||
<p>The CDM is designed to support the conduct of research to identify and evaluate associations between interventions (drug exposure, procedures, healthcare policy changes etc.) and outcomes caused by these interventions (condition occurrences, procedures, drug exposure etc.). Outcomes can be efficacious (benefit) or adverse (safety risk). Often times, specific patient cohorts (e.g., those taking a certain drug or suffering from a certain disease) may be defined for treatments or outcomes, using clinical events (diagnoses, observations, procedures, etc.) that occur in predefined temporal relationships to each other. The CDM, combined with its standardized content (via the Standardized Vocabularies), will ensure that research methods can be systematically applied to produce meaningfully comparable and reproducible results.</p>
|
|
||||||
</div>
|
|
||||||
<div id="design-principles" class="section level2">
|
|
||||||
<h2>Design Principles</h2>
|
|
||||||
<p>The CDM is designed to include all observational health data elements (experiences of the patient receiving health care) that are relevant for analytic use cases to support the generation of reliable scientific evidence about disease natural history, healthcare delivery, effects of medical interventions, the identification of demographic information, health care interventions and outcomes.</p>
|
|
||||||
<p>Therefore, the CDM is designed to store observational data to allow for research, under the following principles:</p>
|
|
||||||
<ul>
|
<ul>
|
||||||
<li><strong>Suitability for purpose:</strong> The CDM aims to provide data organized in a way optimal for analysis, rather than for the purpose of addressing the operational needs of health care providers or payers.</li>
|
<li><a href="https://drive.google.com/open?id=1DaNKe6ivIAZPJeI31VJ-pzNB9wS9hDqu">Google Drive Location</a></li>
|
||||||
<li><strong>Data protection:</strong> All data that might jeopardize the identity and protection of patients, such as names, precise birthdays etc. are limited. Exceptions are possible where the research expressly requires more detailed information, such as precise birth dates for the study of infants.</li>
|
<li><a href="https://docs.google.com/document/d/1WgKePjrI_cGdqn2XQCe1JdGaTzdMqU4p5ihkMt8fcAc/edit?usp=sharing">Running Agenda</a></li>
|
||||||
<li><strong>Design of domains:</strong> The domains are modeled in a person-centric relational data model, where for each record the identity of the person and a date is captured as a minimum.</li>
|
<li><a href="https://github.com/OHDSI/CommonDataModel">CDM Github</a></li>
|
||||||
<li><strong>Rationale for domains:</strong> Domains are identified and separately defined in an entity-relationship model if they have an analysis use case and the domain has specific attributes that are not otherwise applicable. All other data can be preserved as an observation in an entity-attribute-value structure.</li>
|
<li><a href="https://www.ohdsi.org/web/wiki/doku.php?id=documentation:next_cdm:cdm_process">Process for adopting CDM and Vocabulary changes</a></li>
|
||||||
<li><strong>Standardized Vocabularies:</strong> To standardize the content of those records, the CDM relies on the Standardized Vocabularies containing all necessary and appropriate corresponding standard healthcare concepts.</li>
|
|
||||||
<li><strong>Reuse of existing vocabularies:</strong> If possible, these concepts are leveraged from national or industry standardization or vocabulary definition organizations or initiatives, such as the National Library of Medicine, the Department of Veterans’ Affairs, the Center of Disease Control and Prevention, etc.</li>
|
|
||||||
<li><strong>Maintaining source codes:</strong> Even though all codes are mapped to the Standardized Vocabularies, the model also stores the original source code to ensure no information is lost.</li>
|
|
||||||
<li><strong>Technology neutrality:</strong> The CDM does not require a specific technology. It can be realized in any relational database, such as Oracle, SQL Server etc., or as SAS analytical datasets.</li>
|
|
||||||
<li><strong>Scalability:</strong> The CDM is optimized for data processing and computational analysis to accommodate data sources that vary in size, including databases with up to hundreds of millions of persons and billions of clinical observations.</li>
|
|
||||||
<li><strong>Backwards compatibility:</strong> All changes from previous CDMs are clearly delineated in the <a href="https://github.com/OHDSI/CommonDataModel">github repository</a>. Older versions of the CDM can be easily created from the CDMv5, and no information is lost that was present previously.</li>
|
|
||||||
</ul>
|
</ul>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
</div>
|
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|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,342 @@
|
||||||
|
cdmTableName,cdmFieldName,conceptId,conceptName,unitConceptId,unitConceptName,plausibleValueLow,plausibleValueHigh,plausibleGender,isTemporallyConstant,validPrevalenceLow,validPrevalenceHigh
|
||||||
|
MEASUREMENT,MEASUREMENT_CONCEPT_ID,3004410,Hemoglobin A1c/Hemoglobin.total in Blood,8554,percent,4,15,,Yes,,
|
||||||
|
MEASUREMENT,MEASUREMENT_CONCEPT_ID,3036277,Body height,8582,centimeter,1,272,,Yes,,
|
||||||
|
MEASUREMENT,MEASUREMENT_CONCEPT_ID,3016723,Creatinine [Mass/volume] in Serum or Plasma,8840,milligram per deciliter,0.1,10,,Yes,,
|
||||||
|
MEASUREMENT,MEASUREMENT_CONCEPT_ID,3004249,Systolic blood pressure,8876,millimeter mercury column,60,300,,Yes,,
|
||||||
|
MEASUREMENT,MEASUREMENT_CONCEPT_ID,3012888,Diastolic blood pressure,8876,millimeter mercury column,30,200,,Yes,,
|
||||||
|
MEASUREMENT,MEASUREMENT_CONCEPT_ID,3025315,Body weight,9529,kilogram,1,635,,Yes,,
|
||||||
|
MEASUREMENT,MEASUREMENT_CONCEPT_ID,3038553,Body mass index (BMI) [Ratio],9531,kilogram per square meter,10,80,,Yes,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,26662,Testicular hypofunction,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,26935,Disorder of endocrine testis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,30969,Testicular hyperfunction,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,73801,Scrotal varices,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,74322,Benign neoplasm of scrotum,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,78193,Orchitis and epididymitis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,79758,Primary malignant neoplasm of scrotum,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,141917,Balanitis xerotica obliterans,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,192367,Dysplasia of cervix,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,192676,Cervical intraepithelial neoplasia grade 1,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,192683,Uterovaginal prolapse,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,192854,Intramural leiomyoma of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,192858,Ovarian hyperfunction,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,193254,Disorder of vagina,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,193261,Vaginospasm,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,193262,Inflammatory disorder of penis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,193277,Deliveries by cesarean,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,193437,Neoplasm of uncertain behavior of female genital organ,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,193439,Benign neoplasm of body of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,193522,Acute prostatitis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,193530,Follicular cyst of ovary,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,193739,Ovarian failure,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,193818,Calculus of prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,194092,Uterine prolapse without vaginal wall prolapse,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,194286,"Malignant neoplasm of corpus uteri, excluding isthmus",,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,194412,Dysplasia of vagina,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,194420,Endometriosis of fallopian tube,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,194611,Carcinoma in situ of uterine cervix,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,194696,Dysmenorrhea,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,194871,Trichomonal vulvovaginitis,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,194997,Prostatitis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195009,Leukoplakia of penis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195012,Intermenstrual bleeding - irregular,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195197,Primary malignant neoplasm of vulva,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195316,Atypical endometrial hyperplasia,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195321,Postmenopausal bleeding,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195483,Primary malignant neoplasm of penis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195500,Benign neoplasm of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195501,Polycystic ovaries,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195683,Open wound of penis without complication,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195769,Submucous leiomyoma of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195770,Subserous leiomyoma of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195793,Neoplasm of uncertain behavior of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195867,Noninflammatory disorder of the vagina,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,195873,Leukorrhea,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196048,Primary malignant neoplasm of vagina,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196051,Overlapping malignant neoplasm of female genital organs,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196068,Carcinoma in situ of male genital organ,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196157,Induratio penis plastica,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196158,Disorder of penis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196163,Cervicitis and endocervicitis,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196165,Cervical intraepithelial neoplasia grade 2,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196168,Irregular periods,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196359,Primary malignant neoplasm of uterine cervix,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196364,Benign neoplasm of uterine cervix,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196473,Hypertrophy of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196734,Disorder of prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196738,Disorder of male genital organ,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,196758,Tumor of body of uterus affecting pregnancy,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197032,Hyperplasia of prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197039,Male genital organ vascular diseases,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197044,Female infertility associated with anovulation,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197236,Uterine leiomyoma,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197237,Benign neoplasm of prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197507,Primary malignant neoplasm of male genital organ,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197601,Spermatocele,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197605,Inflammatory disorder of male genital organ,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197606,Female infertility of tubal origin,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197607,Excessive and frequent menstruation,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197609,"Cervical, vaginal and vulval inflammatory diseases",,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197610,Cyst of ovary,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,197938,Uterine inertia,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,198082,Overlapping malignant neoplasm of body of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,198108,Benign neoplasm of fallopian tubes and uterine ligaments,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,198194,Female genital organ symptoms,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,198197,Male infertility,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,198198,Polyp of vagina,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,198202,Cystocele,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,198212,Spotting per vagina in pregnancy,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,198363,Candidiasis of vagina,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,198471,Complex endometrial hyperplasia,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,198483,Stricture or atresia of the vagina,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,198803,Benign prostatic hyperplasia,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,198806,Abscess of prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,199067,Female pelvic inflammatory disease,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,199078,Vaginal wall prolapse,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,199752,Secondary malignant neoplasm of ovary,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,199764,Benign neoplasm of ovary,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,199876,Prolapse of female genital organs,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,199877,Mucous polyp of cervix,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,199878,Light and infrequent menstruation,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,199881,Endometriosis of ovary,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200051,Primary malignant neoplasm of ovary,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200052,Primary malignant neoplasm of uterine adnexa,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200147,Atrophy of prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200445,Chronic prostatitis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200452,Disorder of female genital organs,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200461,Endometriosis of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200670,Benign neoplasm of male genital organ,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200675,Neoplasm of uncertain behavior of ovary,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200775,Endometrial hyperplasia,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200779,Polyp of corpus uteri,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200780,Disorder of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200962,Primary malignant neoplasm of prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200970,Carcinoma in situ of prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201072,Benign prostatic hypertrophy without outflow obstruction,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201078,Atrophic vaginitis,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201211,Herpetic vulvovaginitis,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201238,Primary malignant neoplasm of female genital organ,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201244,Benign neoplasm of vagina,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201257,Disorder of endocrine ovary,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201346,Edema of penis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201355,Erosion and ectropion of the cervix,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201527,Neoplasm of uncertain behavior of prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201617,Prostatic cyst,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201625,Malposition of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201801,Primary malignant neoplasm of fallopian tube,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201817,Benign neoplasm of female genital organ,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201823,Benign neoplasm of penis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201907,Edema of male genital organs,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201909,Female infertility,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201913,"Torsion of the ovary, ovarian pedicle or fallopian tube",,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,314409,Vascular disorder of penis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,315586,Priapism,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,433716,Primary malignant neoplasm of testis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,434251,Injury of male external genital organs,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,435315,Torsion of testis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,435648,Retractile testis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,436155,Redundant prepuce and phimosis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,436358,Primary malignant neoplasm of exocervix,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,436366,Benign neoplasm of testis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,436466,Balanoposthitis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,437501,Primary malignant neoplasm of labia majora,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,437655,Undescended testicle,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,438477,Atrophy of testis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,439871,Hemospermia,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,440971,Neoplasm of uncertain behavior of testis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,441068,Torsion of appendix of testis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,441077,Stenosis of cervix,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,441805,Primary malignant neoplasm of endocervix,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,442781,Disorder of uterine cervix,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,443211,Benign prostatic hypertrophy with outflow obstruction,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,443435,Primary uterine inertia,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,443800,Amenorrhea,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,444078,Inflammation of cervix,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,444106,Candidiasis of vulva,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2003947,Closed [percutaneous] [needle] biopsy of prostate,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2003966,Other transurethral prostatectomy,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2003983,Other prostatectomy,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2004031,Other repair of scrotum and tunica vaginalis,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2004063,Unilateral orchiectomy,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2004070,Other repair of testis,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2004090,Excision of varicocele and hydrocele of spermatic cord,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2004164,Local excision or destruction of lesion of penis,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2004263,Other removal of both ovaries and tubes at same operative episode,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2004329,Other bilateral destruction or occlusion of fallopian tubes,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2004342,Removal of both fallopian tubes at same operative episode,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2004443,Closed biopsy of uterus,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2004627,Vaginal suspension and fixation,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109825,"Transurethral electrosurgical resection of prostate, including control of postoperative bleeding, complete (vasectomy, meatotomy, cystourethroscopy, urethral calibration and/or dilation, and internal urethrotomy are included)",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109833,"Laser vaporization of prostate, including control of postoperative bleeding, complete (vasectomy, meatotomy, cystourethroscopy, urethral calibration and/or dilation, internal urethrotomy and transurethral resection of prostate are included if performed)",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109900,"Destruction of lesion(s), penis (eg, condyloma, papilloma, molluscum contagiosum, herpetic vesicle), simple; chemical",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109902,"Destruction of lesion(s), penis (eg, condyloma, papilloma, molluscum contagiosum, herpetic vesicle), simple; cryosurgery",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109905,"Destruction of lesion(s), penis (eg, condyloma, papilloma, molluscum contagiosum, herpetic vesicle), extensive (eg, laser surgery, electrosurgery, cryosurgery, chemosurgery)",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109906,Biopsy of penis, (separate procedure),,,,,Male,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109916,"Circumcision, using clamp or other device with regional dorsal penile or ring block",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109968,Foreskin manipulation including lysis of preputial adhesions and stretching,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109973,"Orchiectomy, simple (including subcapsular), with or without testicular prosthesis, scrotal or inguinal approach",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109981,"Orchiopexy, inguinal approach, with or without hernia repair",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110004,Drainage of scrotal wall abscess,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110011,"Vasectomy, unilateral or bilateral (separate procedure), including postoperative semen examination(s)",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110026,"Biopsy, prostate; needle or punch, single or multiple, any approach",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110039,"Prostatectomy, retropubic radical, with or without nerve sparing; with bilateral pelvic lymphadenectomy, including external iliac, hypogastric, and obturator nodes",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110044,"Laparoscopy, surgical prostatectomy, retropubic radical, including nerve sparing, includes robotic assistance, when performed",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110078,Colposcopy of the vulva,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110116,"Colpopexy, vaginal; extra-peritoneal approach (sacrospinous, iliococcygeus)",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110142,"Laparoscopy, surgical, colpopexy (suspension of vaginal apex)",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110144,Colposcopy of the cervix including upper/adjacent vagina, with biopsy(s) of the cervix and endocervical curettage,,,,,Female,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110169,"Endometrial sampling (biopsy) with or without endocervical sampling (biopsy), without cervical dilation, any method (separate procedure)",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110175,"Total abdominal hysterectomy (corpus and cervix), with or without removal of tube(s), with or without removal of ovary(s)",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110194,Insertion of intrauterine device (IUD),,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110195,Removal of intrauterine device (IUD),,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110203,"Endometrial ablation, thermal, without hysteroscopic guidance",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110222,"Hysteroscopy, surgical; with sampling (biopsy) of endometrium and/or polypectomy, with or without D & C",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110227,"Hysteroscopy, surgical; with endometrial ablation (eg, endometrial resection, electrosurgical ablation, thermoablation)",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110230,"Laparoscopy, surgical, with total hysterectomy, for uterus 250 g or less; with removal of tube(s) and/or ovary(s)",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110307,"Routine obstetric care including antepartum care, vaginal delivery (with or without episiotomy, and/or forceps) and postpartum care",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110315,"Routine obstetric care including antepartum care, cesarean delivery, and postpartum care",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110316,Cesarean delivery only,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110317,Cesarean delivery only, including postpartum care,,,,,Female,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110326,"Treatment of missed abortion, completed surgically; first trimester",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2211747,"Ultrasound, pregnant uterus, real time with image documentation, fetal and maternal evaluation, first trimester (< 14 weeks 0 days), transabdominal approach; single or first gestation",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2211749,"Ultrasound, pregnant uterus, real time with image documentation, fetal and maternal evaluation, after first trimester (> or = 14 weeks 0 days), transabdominal approach; single or first gestation",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2211751,"Ultrasound, pregnant uterus, real time with image documentation, fetal and maternal evaluation plus detailed fetal anatomic examination, transabdominal approach; single or first gestation",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2211753,"Ultrasound, pregnant uterus, real time with image documentation, first trimester fetal nuchal translucency measurement, transabdominal or transvaginal approach; single or first gestation",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2211755,"Ultrasound, pregnant uterus, real time with image documentation, limited (eg, fetal heart beat, placental location, fetal position and/or qualitative amniotic fluid volume), 1 or more fetuses",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2211756,"Ultrasound, pregnant uterus, real time with image documentation, follow-up (eg, re-evaluation of fetal size by measuring standard growth parameters and amniotic fluid volume, re-evaluation of organ system(s) suspected or confirmed to be abnormal on a prev",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2211757,"Ultrasound, pregnant uterus, real time with image documentation, transvaginal",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2211765,"Ultrasound, transvaginal",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2211769,"Ultrasound, scrotum and contents",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2617204,Cervical or vaginal cancer screening, pelvic and clinical breast examination,,,,,Female,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2721063,"Annual gynecological examination, new patient",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2721064,"Annual gynecological examination, established patient",,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2780478,"Resection of Prostate, Percutaneous Endoscopic Approach",,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2780523,"Resection of Prepuce, External Approach",,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4005743,Female sterility,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4005933,"Hypospadias, penile",,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4012343,Vaginal discharge symptom,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4016155,Prostatism,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4021531,Total abdominal hysterectomy,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4032594,Inflammation of scrotum,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4032622,Laparoscopic supracervical hysterectomy,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4038747,Obstetric examination,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4048225,Neoplasm of endometrium,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4050091,Open wound of penis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4051956,Vulvovaginal disease,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4052532,Hysteroscopy,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4054550,Open wound of scrotum and testes,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4056903,Vaginitis associated with another disorder,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4058792,Douche of vagina,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4060207,Vulval irritation,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4060556,"Uterine scar from previous surgery in pregnancy, childbirth and the puerperium",,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4060558,"Uterine scar from previous surgery in pregnancy, childbirth and the puerperium - delivered",,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4060559,"Uterine scar from previous surgery in pregnancy, childbirth and the puerperium with antenatal problem",,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4061050,Subacute and chronic vaginitis,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4071874,Pain in scrotum,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4073700,Transurethral laser prostatectomy,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4081648,Acute vaginitis,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4083772,Echography of scrotum and contents,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4090039,Penile arterial insufficiency,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4092515,"Malignant neoplasm, overlapping lesion of cervix uteri",,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4093346,Large prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4095940,Finding of pattern of menstrual cycle,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4096783,Radical prostatectomy,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4109081,Pain in penis,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4127886,Hysterectomy,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4128329,Menopause present,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4129155,Vaginal bleeding,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4138738,Vaginal hysterectomy,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4140828,Acute vulvitis,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4141940,Endometrial ablation,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4143116,Azoospermia,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4146777,Radical abdominal hysterectomy,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4147021,"Contusion, scrotum or testis",,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4149084,Vaginitis,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4150042,Vaginal ulcer,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4150816,Bicornuate uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4155529,Mechanical complication of intrauterine contraceptive device,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4156113,Malignant neoplasm of body of uterus,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4161944,Low cervical cesarean section,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4162860,Primary malignant neoplasm of body of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4163261,Malignant tumor of prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4171394,Abnormal menstrual cycle,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4171915,Orchitis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4180978,Vulvovaginitis,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4181912,Cone biopsy of cervix,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4194652,Pruritus of vulva,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4199600,Candidal balanitis,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4234536,Transurethral prostatectomy,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4235215,Swelling of testicle,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4238715,Removal of intrauterine device,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4243919,Incision of ovary,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4260520,Balanitis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4270932,Pain in testicle,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4275113,Insertion of intrauterine contraceptive device,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4279913,Primary ovarian failure,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4281030,Secondary malignant neoplasm of right ovary,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4294393,Ulcer of penis,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4294805,Laparoscopic-assisted vaginal hysterectomy,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4295261,Postmenopausal state,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4303258,Bacterial vaginosis,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4306780,Gynecologic examination,,,,,Female,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4310552,Orchidopexy,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4320332,Hydrocele of tunica vaginalis,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4321575,Lysis of penile adhesions,,,,,Male,,,
|
||||||
|
PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4330583,Vasectomy,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,4339088,Testicular mass,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,40481080,Benign localized hyperplasia of prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,40482030,Dysplasia of prostate,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,40482406,Low lying placenta,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,40483613,Inflammatory disease of female genital structure,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,40490888,Herniation of rectum into vagina,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,42709954,Phimosis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,45757415,Benign endometrial hyperplasia,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,45766654,Disorder of skin of penis,,,,,Male,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,45770892,Primary malignant neoplasm of uterus,,,,,Female,,,
|
||||||
|
CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,45772671,Nodular prostate without urinary obstruction,,,,,Male,,,
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,4006969,Acute respiratory disease,,,,,,Yes,0.1703,1
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,4134440,Visual system disorder,,,,,,Yes,0.1181,1
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,316866,Hypertensive disorder,,,,,,Yes,0.0913,0.8215
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,432867,Hyperlipidemia,,,,,,Yes,0.0712,0.6412
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,321588,Heart disease,,,,,,Yes,0.061,0.5491
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,80180,Osteoarthritis,,,,,,Yes,0.0584,0.5252
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,321052,Peripheral vascular disease,,,,,,Yes,0.0426,0.3832
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,81902,Urinary tract infectious disease,,,,,,Yes,0.0412,0.371
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,440383,Depressive disorder,,,,,,Yes,0.0392,0.3531
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,201820,Diabetes mellitus,,,,,,Yes,0.039,0.3514
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,433736,Obesity,,,,,,Yes,0.038,0.3422
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,318800,Gastroesophageal reflux disease,,,,,,Yes,0.0337,0.3033
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,443392,Malignant neoplastic disease,,,,,,Yes,0.0326,0.2932
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,255848,Pneumonia,,,,,,Yes,0.0218,0.1966
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,317576,Coronary arteriosclerosis,,,,,,Yes,0.0206,0.1852
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,4185932,Ischemic heart disease,,,,,,Yes,0.0201,0.1813
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,255573,Chronic obstructive lung disease,,,,,,Yes,0.0194,0.1742
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,4030518,Renal impairment,,,,,,Yes,0.0174,0.1568
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,316139,Heart failure,,,,,,Yes,0.0161,0.1452
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,381591,Cerebrovascular disease,,,,,,Yes,0.0142,0.1274
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,192671,Gastrointestinal hemorrhage,,,,,,Yes,0.0135,0.1219
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,313217,Atrial fibrillation,,,,,,Yes,0.0128,0.1155
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,4182210,Dementia,,,,,,Yes,0.0086,0.0773
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,444247,Venous thrombosis,,,,,,Yes,0.0082,0.0737
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,438409,Attention deficit hyperactivity disorder,,,,,,Yes,0.0078,0.0706
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,4279309,Substance abuse,,,,,,Yes,0.0063,0.0568
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,140168,Psoriasis,,,,,,Yes,0.0055,0.0494
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,4212540,Chronic liver disease,,,,,,Yes,0.0053,0.0476
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,200962,Primary malignant neoplasm of prostate,,,,,,Yes,0.0052,0.0471
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,4112853,Malignant tumor of breast,,,,,,Yes,0.0047,0.0421
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,80809,Rheumatoid arthritis,,,,,,Yes,0.0045,0.0405
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,4044013,Hematologic neoplasm,,,,,,Yes,0.0037,0.0331
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,4104000,Lesion of liver,,,,,,Yes,0.0029,0.0265
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,440417,Pulmonary embolism,,,,,,Yes,0.0024,0.022
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,435783,Schizophrenia,,,,,,Yes,0.0021,0.0186
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,443388,Malignant tumor of lung,,,,,,Yes,0.0021,0.0185
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,4180790,Malignant tumor of colon,,,,,,Yes,0.0019,0.0173
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,197494,Viral hepatitis C,,,,,,Yes,0.0017,0.0155
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,432571,Malignant lymphoma,,,,,,Yes,0.0016,0.0143
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,81893,Ulcerative colitis,,,,,,Yes,0.0014,0.0128
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,197508,Malignant tumor of urinary bladder,,,,,,Yes,0.0013,0.0113
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,201606,Crohn's disease,,,,,,Yes,0.0012,0.0112
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,40481902,Malignant neoplasm of anorectum,,,,,,Yes,0.001,0.0089
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,439727,Human immunodeficiency virus infection,,,,,,Yes,0.0006,0.0057
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,9201,Inpatient visit,,,,,,Yes,,
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,9202,Outpatient visit,,,,,,Yes,,
|
||||||
|
CONDITION,CONDITION_CONCEPT_ID,9203,ER visit,,,,,,Yes,,
|
||||||
|
|
|
@ -0,0 +1,334 @@
|
||||||
|
cdmTableName,cdmFieldName,isRequired,isRequiredThreshold,cdmDatatype,cdmDatatypeThreshold,userGuidance,etlConventions,isPrimaryKey,isPrimaryKeyThreshold,isForeignKey,isForeignKeyThreshold,fkTableName,fkFieldName,fkDomain,fkDomainThreshold,fkClass,fkClassThreshold,isStandardValidConcept,isStandardValidConceptThreshold,measureValueCompleteness,measureValueCompletenessThreshold,standardConceptRecordCompleteness,standardConceptRecordCompletenessThreshold,sourceConceptRecordCompleteness,sourceConceptRecordCompletenessThreshold,sourceValueCompleteness,sourceValueCompletenessThreshold,standardConceptFieldName,plausibleValueLow,plausibleValueLowThreshold,plausibleValueHigh,plausibleValueHighThreshold,plausibleTemporalAfterTableName,plausibleTemporalAfterFieldName,plausibleTemporalAfterThreshold,plausibleDuringLife,plausibleDuringLifeThreshold
|
||||||
|
PERSON,person_id,Yes,0,integer,0,It is assumed that every person with a different unique identifier is in fact a different person and should be treated independently.,Any person linkage that needs to occur to identify unique persons should be done prior to ETL.,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PERSON,gender_concept_id,Yes,0,integer,0,This field is meant to capture the biological sex at birth of the Person. This field should not be used to study gender identity issues.,Use the gender or sex value present in the data under the assumption that it is the biological sex at birth. If the source data captures gender identity it should be stored in the OBSERVATION table.,No,,Yes,0,CONCEPT,CONCEPT_ID,Gender,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
PERSON,year_of_birth,Yes,0,integer,0,,"For data sources with date of birth, the year is extracted. For data sources where the year of birth is not available, the approximate year of birth is derived based on any age group categorization available.",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,1850,0,YEAR(GETDATE())+1,0,,,,No,
|
||||||
|
PERSON,month_of_birth,No,,integer,0,,"For data sources that provide the precise date of birth, the month is extracted and stored in this field.",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,1,0,12,0,,,,No,
|
||||||
|
PERSON,day_of_birth,No,,integer,0,,"For data sources that provide the precise date of birth, the day is extracted and stored in this field.",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,1,0,31,0,,,,No,
|
||||||
|
PERSON,birth_datetime,No,,datetime,0,Compute age using birth_datetime.,"For data sources that provide the precise datetime of birth, store that value in this field. If birth_datetime is not provided in the source, use the following logic to infer the date: If day_of_birth is null and month_of_birth is not null then use month/1/year. If month_of_birth is null then use 1/day/year, if day_of_birth is null and month_of_birth is null then 1/1/year. If time of birth is not given use midnight (00:00:0000).",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1850-01-01',0,"DATEADD(dd,1,GETDATE())",0,,,,No,
|
||||||
|
PERSON,race_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Race,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
PERSON,ethnicity_concept_id,Yes,0,integer,0,"Ethnic backgrounds as subsets of race. The OMOP CDM adheres to the OMB standards so only Concepts that represent ""Hispanic"" and ""Not Hispanic"" are stored here. If a source has more granular ethnicity information it can be found in the field ethnicity_source_value.",Ethnicity in the OMOP CDM follows the OMB Standards for Data on Race and Ethnicity: Only distinctions between Hispanics and Non-Hispanics are made. If a source provides more granular ethnicity information it should be stored in the field ethnicity_source_value.,No,,Yes,0,CONCEPT,CONCEPT_ID,Ethnicity,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
PERSON,location_id,No,,integer,0,The location refers to the physical address of the person.,"Put the location_id from the LOCATION table here that represents the most granular location information for the person. This could be zip code, state, or county for example.",No,,Yes,0,LOCATION,LOCATION_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PERSON,provider_id,No,,integer,0,The Provider refers to the last known primary care provider (General Practitioner).,Put the provider_id from the PROVIDER table of the last known general practitioner of the person.,No,,Yes,0,PROVIDER,PROVIDER_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PERSON,care_site_id,No,,integer,0,The Care Site refers to where the Provider typically provides the primary care.,,No,,Yes,0,CARE_SITE,CARE_SITE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PERSON,person_source_value,No,,varchar(50),0,Use this field to link back to persons in the source data. This is typically used for error checking of ETL logic.,Some use cases require the ability to link back to persons in the source data. This field allows for the storing of the person value as it appears in the source.,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PERSON,gender_source_value,No,,varchar(50),0,This field is used to store the biological sex of the person from the source data. It is not intended for use in standard analytics but for reference only.,Put the biological sex of the person as it appears in the source data.,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,GENDER_CONCEPT_ID,,,,,,,,No,
|
||||||
|
PERSON,gender_source_concept_id,No,,Integer,0,,"If the source data codes biological sex in a non-standard vocabulary, store the concept_id here.",No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,Yes,0,No,,,,,,,,,,No,
|
||||||
|
PERSON,race_source_value,No,,varchar(50),0,This field is used to store the race of the person from the source data. It is not intended for use in standard analytics but for reference only.,Put the race of the person as it appears in the source data.,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,RACE_CONCEPT_ID,,,,,,,,No,
|
||||||
|
PERSON,race_source_concept_id,No,,Integer,0,,If the source data codes race in an OMOP supported vocabulary store the concept_id here.,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,Yes,0,No,,,,,,,,,,No,
|
||||||
|
PERSON,ethnicity_source_value,No,,varchar(50),0,This field is used to store the ethnicity of the person from the source data. It is not intended for use in standard analytics but for reference only.,"If the person has an ethnicity other than the OMB standard of ""Hispanic"" or ""Not Hispanic"" store that value from the source data here.",No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,ETHNICITY_CONCEPT_ID,,,,,,,,No,
|
||||||
|
PERSON,ethnicity_source_concept_id,No,,Integer,0,,"If the source data codes ethnicity in an OMOP supported vocabulary, store the concept_id here.",No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,Yes,0,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION_PERIOD,observation_period_id,Yes,0,integer,0,A Person can have multiple discrete observations periods which are identified by the Observation_Period_Id. It is assumed that the observation period covers the period of time for which we know events occurred for the Person. In the context of the Common Data Model the absence of events during an observation period implies that the event did not occur.,"Assign a unique observation_period_id to each discrete observation period for a Person. An observation period should the length of time for which we know events occurred for the Person. It may take some logic to define an observation period, especially when working with EHR or registry data. Often if no enrollment or coverage information is given an observation period is defined as the time between the earliest record and the latest record available for a person.",Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION_PERIOD,person_id,Yes,0,integer,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION_PERIOD,observation_period_start_date,Yes,0,date,0,Use this date to determine the start date of the period for which we can assume that all events for a Person are recorded and any absense of records indicates an absence of events.,"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 US claims, the observation period can be considered as the time period the person is enrolled with an insurer. If a Person switches plans but stays with the same insurer, that change would be captured in payer_plan_period.",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
OBSERVATION_PERIOD,observation_period_end_date,Yes,0,date,0,Use this date to determine the end date of the period for which we can assume that all events for a Person are recorded and any absense of records indicates an absence of events.,It is often the case that the idea of observation periods does not exist in source data. In those cases the observation_period_start_end_date can be inferred as the latest event date available for the Person. The event dates include insurance enrollment dates.,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,OBSERVATION_PERIOD,OBSERVATION_PERIOD_START_DATE,0,Yes,0
|
||||||
|
OBSERVATION_PERIOD,period_type_concept_id,Yes,0,Integer,0,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 or if it was determined from EHR healthcare encounters.,Choose the observation_period_type_concept_id that best represents how the period was determined.,No,,Yes,0,CONCEPT,CONCEPT_ID,Type Concept,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,visit_occurrence_id,Yes,0,integer,0,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,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,person_id,Yes,0,integer,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,visit_concept_id,Yes,0,integer,0,"This field contains a concept id representing the kind of visit, like inpatient or outpatient.","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. It is often the case that some logic should be written for how to define visits and how to assign Visit_Concept_Id. In US claims outpatient visits that appear to occur within the time period of an inpatient visit can be rolled into one with the same Visit_Occurrence_Id. In EHR data inpatient visits that are within one day of each other may be strung together to create one visit. It will all depend on the source data and how encounter records should be translated to visit occurrences.",No,,Yes,0,CONCEPT,CONCEPT_ID,Visit,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,visit_start_date,Yes,0,date,0,"For inpatient visits, the start date is typically the admission date. For outpatient visits the start date and end date will be the same.","When populating visit_start_date, you will first have to make decisions on how to define visits. In some cases visits in the source data can be strung together if there are one or fewer days between them.",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
VISIT_OCCURRENCE,visit_start_datetime,No,,datetime,0,,"If no time is given for the start date of a visit, set it to midnight (00:00:0000).",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
VISIT_OCCURRENCE,visit_end_date,Yes,0,date,0,For inpatient visits the end date is typically the discharge date.,"Visit end dates are mandatory. If end dates are not provided in the source there are three ways in which to derive them:
|
||||||
|
Outpatient Visit: visit_end_datetime = visit_start_datetime
|
||||||
|
Emergency Room Visit: visit_end_datetime = visit_start_datetime
|
||||||
|
Inpatient Visit: Usually there is information about discharge. If not, you should be able to derive the end date from the sudden decline of activity or from the absence of inpatient procedures/drugs.
|
||||||
|
Non-hospital institution Visits: Particularly for claims data, if end dates are not provided assume the visit is for the duration of month that it occurs.
|
||||||
|
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,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,VISIT_OCCURRENCE,VISIT_START_DATE,0,Yes,0
|
||||||
|
VISIT_OCCURRENCE,visit_end_datetime,No,,datetime,0,,"If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,VISIT_OCCURRENCE,VISIT_START_DATETIME,0,Yes,0
|
||||||
|
VISIT_OCCURRENCE,visit_type_concept_id,Yes,0,Integer,0,"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.",No,,Yes,0,CONCEPT,CONCEPT_ID,Type Concept,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,provider_id,No,,integer,0,There will only be one provider per visit. If multiple providers are associated with a visit that information can be found 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 table.",No,,No,,PROVIDER,PROVIDER_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,care_site_id,No,,integer,0,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,,No,,CARE_SITE,CARE_SITE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,visit_source_value,No,,varchar(50),0,"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,,,,,,,,No,,Yes,100,No,,No,,Yes,0,VISIT_CONCEPT_ID,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,visit_source_concept_id,No,,integer,0,,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,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,Yes,0,No,,,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,admitting_source_concept_id,No,,integer,0,"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.",No,,Yes,0,CONCEPT,CONCEPT_ID,Visit,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,admitting_source_value,No,,varchar(50),0,,"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,,,,,,,,No,,Yes,100,No,,No,,Yes,0,ADMITTING_SOURCE_CONCEPT_ID,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,discharge_to_concept_id,No,,integer,0,"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 discharged to home or sent to a long-term care facility, for example.","If available, map the discharge_to_source_value to a standard concept in the visit domain.",No,,Yes,0,CONCEPT,CONCEPT_ID,Visit,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,discharge_to_source_value,No,,varchar(50),0,,"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,,,,,,,,No,,Yes,100,No,,No,,Yes,0,DISCHARGE_TO_CONCEPT_ID,,,,,,,,No,
|
||||||
|
VISIT_OCCURRENCE,preceding_visit_occurrence_id,No,,integer,0,Use this field to find the visit that occured for the person prior to the given visit. There could be a few days or a few years in between.,"The preceding_visit_id 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,0,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_OCCURRENCE,condition_occurrence_id,Yes,0,bigint,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_OCCURRENCE,person_id,Yes,0,bigint,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_OCCURRENCE,condition_concept_id,Yes,0,integer,0,"The CONDITION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies",,No,,Yes,0,CONCEPT,CONCEPT_ID,Condition,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_OCCURRENCE,condition_start_date,Yes,0,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
CONDITION_OCCURRENCE,condition_start_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
CONDITION_OCCURRENCE,condition_end_date,No,,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,CONDITION_OCCURRENCE,CONDITION_START_DATE,0,Yes,0
|
||||||
|
CONDITION_OCCURRENCE,condition_end_datetime,No,,datetime,0,,should not be inferred,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,CONDITION_OCCURRENCE,CONDITION_START_DATETIME,0,Yes,0
|
||||||
|
CONDITION_OCCURRENCE,condition_type_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Type Concept,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_OCCURRENCE,condition_status_concept_id,No,,integer,0,,"Presently, there is no designated vocabulary, domain, or class that represents condition status. The following concepts from SNOMED are recommended:
|
||||||
|
Admitting diagnosis: 4203942
|
||||||
|
Final diagnosis: 4230359 (should also be used for discharge diagnosis
|
||||||
|
Preliminary diagnosis: 4033240",No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_OCCURRENCE,stop_reason,No,,varchar(20),0,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.,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_OCCURRENCE,provider_id,No,,integer,0,,,No,,Yes,0,PROVIDER,PROVIDER_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_OCCURRENCE,visit_occurrence_id,No,,integer,0,,,No,,Yes,0,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_OCCURRENCE,visit_detail_id,No,,integer,0,,,No,,Yes,0,VISIT_DETAIL,VISIT_DETAIL_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_OCCURRENCE,condition_source_value,No,,varchar(50),0,"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 Condition necessary for a given analytic use case. Consider using CONDITION_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. ",This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,CONDITION_CONCEPT_ID,,,,,,,,No,
|
||||||
|
CONDITION_OCCURRENCE,condition_source_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,Yes,0,No,,,,,,,,,,No,
|
||||||
|
CONDITION_OCCURRENCE,condition_status_source_value,No,,varchar(50),0,,This code is mapped to a Standard Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,CONDITION_STATUS_CONCEPT_ID,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,drug_exposure_id,Yes,0,bigint,0,,,Yes,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,person_id,Yes,0,bigint,0,,,No,,Yes,,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,drug_concept_id,Yes,0,integer,0,,,No,,Yes,,CONCEPT,CONCEPT_ID,Drug,,,,Yes,,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,drug_exposure_start_date,Yes,0,date,0,,"Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration procedure was recorded.",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',,"DATEADD(dd,1,GETDATE())",,PERSON,BIRTH_DATETIME,,Yes,0
|
||||||
|
DRUG_EXPOSURE,drug_exposure_start_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',,"DATEADD(dd,1,GETDATE())",,PERSON,BIRTH_DATETIME,,Yes,0
|
||||||
|
DRUG_EXPOSURE,drug_exposure_end_date,Yes,0,date,0,,"The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for the patient. This could be that the duration of DRUG_SUPPLY was reached (in which case DRUG_EXPOSURE_END_DATETIME = DRUG_EXPOSURE_START_DATETIME + DAYS_SUPPLY -1 day), or because the exposure was stopped (medication changed, medication discontinued, etc.) When the native data suggests a drug exposure has a days supply less than 0, drop the record as unknown if a person has received the drug or not (THEMIS issue #24). If a patient has multiple records on the same day for the same drug or procedures the ETL should not de-dupe them unless there is probable reason to believe the item is a true data duplicate (THEMIS issue #14). Depending on different sources, it could be a known or an inferred date and denotes the last day at which the patient was still exposed to Drug.",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',,"DATEADD(dd,1,GETDATE())",,DRUG_EXPOSURE,DRUG_EXPOSURE_START_DATE,,Yes,0
|
||||||
|
DRUG_EXPOSURE,drug_exposure_end_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',,"DATEADD(dd,1,GETDATE())",,DRUG_EXPOSURE,DRUG_EXPOSURE_START_DATETIME,,Yes,0
|
||||||
|
DRUG_EXPOSURE,verbatim_end_date,No,,date,0,You can use the TYPE_CONCEPT_ID to delineate between prescriptions written vs. prescriptions dispensed vs. medication history vs. patient-reported exposure,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',,"DATEADD(dd,1,GETDATE())",,DRUG_EXPOSURE,DRUG_EXPOSURE_START_DATE,,Yes,0
|
||||||
|
DRUG_EXPOSURE,drug_type_concept_id,Yes,0,integer,0,,,No,,Yes,,CONCEPT,CONCEPT_ID,Type Concept,,,,Yes,,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,stop_reason,No,,varchar(20),0,," Reasons include regimen completed, changed, removed, etc.",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,refills,No,,integer,0,"The content of the refills field determines the current number of refills, not the number of remaining refills. For example, for a drug prescription with 2 refills, the content of this field for the 3 Drug Exposure events are null, 1 and 2.",,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,0,,12,,,,,No,
|
||||||
|
DRUG_EXPOSURE,quantity,No,,float,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,0,,1095,,,,,No,
|
||||||
|
DRUG_EXPOSURE,days_supply,No,,integer,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,0,,365,,,,,No,
|
||||||
|
DRUG_EXPOSURE,sig,No,,varchar(MAX),0,(and printed on the container),,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,route_concept_id,No,,integer,0,"Route information can also be inferred from the Drug product itself by determining the Drug Form of the Concept, creating some partial overlap of the same type of information. Therefore, route information should be stored in DRUG_CONCEPT_ID (as a drug with corresponding Dose Form). The ROUTE_CONCEPT_ID could be used for storing more granular forms e.g. 'Intraventricular cardiac'.",,No,,Yes,,CONCEPT,CONCEPT_ID,Route,,,,Yes,,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,lot_number,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,provider_id,No,,integer,0,,,No,,Yes,,PROVIDER,PROVIDER_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,visit_occurrence_id,No,,integer,0,,,No,,Yes,,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,visit_detail_id,No,,integer,0,,,No,,Yes,,VISIT_DETAIL,VISIT_DETAIL_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,drug_source_value,No,,varchar(50),0,,"This code is mapped to a Standard Drug concept in the Standardized Vocabularies and the original code is, stored here for reference.",No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,,DRUG_CONCEPT_ID,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,drug_source_concept_id,No,,integer,0,,,No,,Yes,,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,Yes,,No,,,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,route_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,,ROUTE_CONCEPT_ID,,,,,,,,No,
|
||||||
|
DRUG_EXPOSURE,dose_unit_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROCEDURE_OCCURRENCE,procedure_occurrence_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROCEDURE_OCCURRENCE,person_id,Yes,0,integer,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROCEDURE_OCCURRENCE,procedure_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Procedure,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
PROCEDURE_OCCURRENCE,procedure_date,Yes,0,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
PROCEDURE_OCCURRENCE,procedure_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
PROCEDURE_OCCURRENCE,procedure_type_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Type Concept,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
PROCEDURE_OCCURRENCE,modifier_concept_id,No,,integer,0,"These concepts are typically distinguished by 'Modifier' concept classes (e.g., 'CPT4 Modifier' as part of the 'CPT4' vocabulary).",,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
PROCEDURE_OCCURRENCE,quantity,No,,integer,0,"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 (THEMIS issue #26).",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,1,0,,,,,,No,
|
||||||
|
PROCEDURE_OCCURRENCE,provider_id,No,,integer,0,,,No,,No,,PROVIDER,PROVIDER_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROCEDURE_OCCURRENCE,visit_occurrence_id,No,,integer,0,,,No,,No,,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROCEDURE_OCCURRENCE,visit_detail_id,No,,integer,0,,,No,,No,,VISIT_DETAIL,VISIT_DETAIL_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROCEDURE_OCCURRENCE,procedure_source_value,No,,varchar(50),0,,"This code is mapped to a standard procedure Concept in the Standardized Vocabularies and the original code is, stored here for reference. Procedure source codes are typically ICD-9-Proc, CPT-4, HCPCS or OPCS-4 codes.",No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,PROCEDURE_CONCEPT_ID,,,,,,,,No,
|
||||||
|
PROCEDURE_OCCURRENCE,procedure_source_concept_id,No,,integer,0,,,No,,No,,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,Yes,0,No,,,,,,,,,,No,
|
||||||
|
PROCEDURE_OCCURRENCE,modifier_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,MODIFIER_CONCEPT_ID,,,,,,,,No,
|
||||||
|
DEVICE_EXPOSURE,device_exposure_id,Yes,0,bigint,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DEVICE_EXPOSURE,person_id,Yes,0,bigint,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DEVICE_EXPOSURE,device_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Device,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
DEVICE_EXPOSURE,device_exposure_start_date,Yes,0,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
DEVICE_EXPOSURE,device_exposure_start_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
DEVICE_EXPOSURE,device_exposure_end_date,No,,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,DEVICE_EXPOSURE,DEVICE_EXPOSURE_START_DATE,0,Yes,0
|
||||||
|
DEVICE_EXPOSURE,device_exposure_end_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,DEVICE_EXPOSURE,DEVICE_EXPOSURE_START_DATETIME,0,Yes,0
|
||||||
|
DEVICE_EXPOSURE,device_type_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Type Concept,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
DEVICE_EXPOSURE,unique_device_id,No,,varchar(50),0,,"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,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DEVICE_EXPOSURE,quantity,No,,integer,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,1,0,,,,,,No,
|
||||||
|
DEVICE_EXPOSURE,provider_id,No,,integer,0,,,No,,Yes,0,PROVIDER,PROVIDER_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DEVICE_EXPOSURE,visit_occurrence_id,No,,integer,0,,,No,,Yes,0,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DEVICE_EXPOSURE,visit_detail_id,No,,integer,0,,,No,,Yes,0,VISIT_DETAIL,VISIT_DETAIL_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DEVICE_EXPOSURE,device_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,DEVICE_CONCEPT_ID,,,,,,,,No,
|
||||||
|
DEVICE_EXPOSURE,device_source_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,Yes,0,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,measurement_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,person_id,Yes,0,integer,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,measurement_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Measurement,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,measurement_date,Yes,0,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,No,
|
||||||
|
MEASUREMENT,measurement_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,measurement_time,No,,varchar(10),0,This is present for backwards compatibility and will be deprecated in an upcoming version,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,measurement_type_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Type Concept,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,operator_concept_id,No,,integer,0,"The meaning of Concept 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 =.","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):
|
||||||
|
1925-7 Base excess in Arterial blood by calculation
|
||||||
|
1927-3 Base excess in Venous blood by calculation Operators are <, <=, =, >=, > and these concepts belong to the 'Meas Value Operator' domain.
|
||||||
|
8632-2 QRS-Axis
|
||||||
|
11555-0 Base excess in Blood by calculation
|
||||||
|
1926-5 Base excess in Capillary blood by calculation
|
||||||
|
28638-5 Base excess in Arterial cord blood by calculation
|
||||||
|
28639-3 Base excess in Venous cord blood by calculation
|
||||||
|
THEMIS issue #16",No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,value_as_number,No,,float,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,value_as_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,unit_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Unit,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,range_low,No,,float,0,Ranges have the same unit as the VALUE_AS_NUMBER.,If reference ranges for upper and lower limit of normal as provided (typically by a laboratory) these are stored in the RANGE_HIGH and RANGE_LOW fields. Ranges have the same unit as the VALUE_AS_NUMBER.,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,range_high,No,,float,0,Ranges have the same unit as the VALUE_AS_NUMBER.,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,provider_id,No,,integer,0,,,No,,Yes,0,PROVIDER,PROVIDER_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,visit_occurrence_id,No,,integer,0,,,No,,Yes,0,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,visit_detail_id,No,,integer,0,,,No,,Yes,0,VISIT_DETAIL,VISIT_DETAIL_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,measurement_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,MEASUREMENT_CONCEPT_ID,,,,,,,,No,
|
||||||
|
MEASUREMENT,measurement_source_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,Yes,0,No,,,,,,,,,,No,
|
||||||
|
MEASUREMENT,unit_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,UNIT_CONCEPT_ID,,,,,,,,No,
|
||||||
|
MEASUREMENT,value_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,visit_detail_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,person_id,Yes,0,integer,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,visit_detail_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Visit,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,visit_detail_start_date,Yes,0,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
VISIT_DETAIL,visit_detail_start_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
VISIT_DETAIL,visit_detail_end_date,Yes,0,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,VISIT_OCCURRENCE,VISIT_DETAIL_START_DATE,0,Yes,0
|
||||||
|
VISIT_DETAIL,visit_detail_end_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,VISIT_OCCURRENCE,VISIT_DETAIL_START_DATETIME,0,Yes,0
|
||||||
|
VISIT_DETAIL,visit_detail_type_concept_id,Yes,0,Integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Type Concept,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,provider_id,No,,integer,0,,,No,,Yes,0,PROVIDER,PROVIDER_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,care_site_id,No,,integer,0,,,No,,Yes,0,CARE_SITE,CARE_SITE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,visit_detail_source_value,No,,string(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,VISIT_DETAIL_CONCEPT_ID,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,visit_detail_source_concept_id,No,,Integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,Yes,0,No,,,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,admitting_source_value,No,,Varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,ADMITTING_SOURCE_CONCEPT_ID,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,admitting_source_concept_id,No,,Integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,Yes,0,Yes,0,No,,,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,discharge_to_source_value,No,,Varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,DISCHARGE_TO_CONCEPT_ID,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,discharge_to_concept_id,No,,Integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,preceding_visit_detail_id,No,,Integer,0,,,No,,Yes,0,VISIT_DETAIL,VISIT_DETAIL_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,visit_detail_parent_id,No,,Integer,0,,,No,,Yes,0,VISIT_DETAIL,VISIT_DETAIL_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
VISIT_DETAIL,visit_occurrence_id,Yes,0,Integer,0,,,No,,Yes,0,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE,note_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE,person_id,Yes,0,integer,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE,note_date,Yes,0,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,No,
|
||||||
|
NOTE,note_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,No,
|
||||||
|
NOTE,note_type_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Type Concept,0,,,Yes,0,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE,note_class_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE,note_title,No,,varchar(250),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE,note_text,Yes,0,varchar(MAX),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE,encoding_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE,language_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE,provider_id,No,,integer,0,,,No,,Yes,0,PROVIDER,PROVIDER_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE,visit_occurrence_id,No,,integer,0,,,No,,Yes,0,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE,visit_detail_id,No,,integer,0,,,No,,Yes,0,VISIT_DETAIL,VISIT_DETAIL_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE,note_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,note_nlp_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,note_id,Yes,0,integer,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,section_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,snippet,No,,varchar(250),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,offset,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,lexical_variant,Yes,0,varchar(250),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,note_nlp_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,note_nlp_source_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,nlp_system,No,,varchar(250),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,nlp_date,Yes,0,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,nlp_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,,,,No,
|
||||||
|
NOTE_NLP,term_exists,No,,varchar(1),0,,"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,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,term_temporal,No,,varchar(50),0,,"Term_temporal is to indicate if a condition is <20>present<6E> or just in the <20>past<73>. The following would be past:
|
||||||
|
History = true
|
||||||
|
Concept_date = anything before the time of the report",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
NOTE_NLP,term_modifiers,No,,varchar(2000),0,,"For the modifiers that are there, they would have to have these values:
|
||||||
|
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. A list of allowable modifiers (e.g., signature for medications) and their possible values will be standardized later.",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,observation_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,person_id,Yes,0,integer,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,observation_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,observation_date,Yes,0,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,No,
|
||||||
|
OBSERVATION,observation_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,No,
|
||||||
|
OBSERVATION,observation_type_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Type Concept,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,value_as_number,No,,float,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,value_as_string,No,,varchar(60),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,value_as_concept_id,No,,Integer,0,,"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, ICD9CM V17.5 concept_id 44828510 'Family history of asthma' has a 'Maps to' relationship to 4167217 'Family history of clinical finding' as well as a 'Maps to value' record to 317009 'Asthma'.",No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,qualifier_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,unit_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Unit,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,provider_id,No,,integer,0,,,No,,Yes,0,PROVIDER,PROVIDER_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,visit_occurrence_id,No,,integer,0,,,No,,Yes,0,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,visit_detail_id,No,,integer,0,,,No,,Yes,0,VISIT_DETAIL,VISIT_DETAIL_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,observation_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,OBSERVATION_CONCEPT_ID,,,,,,,,No,
|
||||||
|
OBSERVATION,observation_source_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,Yes,0,No,,,,,,,,,,No,
|
||||||
|
OBSERVATION,unit_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,UNIT_CONCEPT_ID,,,,,,,,No,
|
||||||
|
OBSERVATION,qualifier_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,QUALIFIER_CONCEPT_ID,,,,,,,,No,
|
||||||
|
SPECIMEN,specimen_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
SPECIMEN,person_id,Yes,0,integer,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
SPECIMEN,specimen_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
SPECIMEN,specimen_type_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Type Concept,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
SPECIMEN,specimen_date,Yes,0,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,No,
|
||||||
|
SPECIMEN,specimen_datetime,No,,datetime,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,No,
|
||||||
|
SPECIMEN,quantity,No,,float,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,1,0,,,,,,No,
|
||||||
|
SPECIMEN,unit_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
SPECIMEN,anatomic_site_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
SPECIMEN,disease_status_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
SPECIMEN,specimen_source_id,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
SPECIMEN,specimen_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,SPECIMEN_CONCEPT_ID,,,,,,,,No,
|
||||||
|
SPECIMEN,unit_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,UNIT_CONCEPT_ID,,,,,,,,No,
|
||||||
|
SPECIMEN,anatomic_site_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,ANATOMIC_SITE_CONCEPT_ID,,,,,,,,No,
|
||||||
|
SPECIMEN,disease_status_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,DISEASE_STATUS_CONCEPT_ID,,,,,,,,No,
|
||||||
|
FACT_RELATIONSHIP,domain_concept_id_1,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
FACT_RELATIONSHIP,fact_id_1,Yes,0,integer,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
FACT_RELATIONSHIP,domain_concept_id_2,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
FACT_RELATIONSHIP,fact_id_2,Yes,0,integer,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
FACT_RELATIONSHIP,relationship_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
LOCATION,location_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
LOCATION,address_1,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
LOCATION,address_2,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
LOCATION,city,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
LOCATION,state,No,,varchar(2),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
LOCATION,zip,No,,varchar(9),0,,"Zip codes are handled as strings of up to 9 characters length. For US addresses, these represent either a 3-digit abbreviated Zip code as provided by many sources for patient protection reasons, the full 5-digit Zip or the 9-digit (ZIP + 4) codes. Unless for specific reasons analytical methods should expect and utilize only the first 3 digits. For international addresses, different rules apply.",No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
LOCATION,county,No,,varchar(20),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
LOCATION,location_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CARE_SITE,care_site_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CARE_SITE,care_site_name,No,,varchar(255),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CARE_SITE,place_of_service_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
CARE_SITE,location_id,No,,integer,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CARE_SITE,care_site_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CARE_SITE,place_of_service_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROVIDER,provider_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROVIDER,provider_name,No,,varchar(255),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROVIDER,npi,No,,varchar(20),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROVIDER,dea,No,,varchar(20),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROVIDER,specialty_concept_id,No,,integer,0,,"If a Provider has more than one Specialty, the main or most often exerted specialty should be recorded.",No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
PROVIDER,care_site_id,No,,integer,0,,,No,,Yes,0,CARE_SITE,CARE_SITE_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROVIDER,year_of_birth,No,,integer,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROVIDER,gender_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Gender,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
PROVIDER,provider_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PROVIDER,specialty_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,SPECIALTY_CONCEPT_ID,,,,,,,,No,
|
||||||
|
PROVIDER,specialty_source_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,Yes,0,No,,,,,,,,,,No,
|
||||||
|
PROVIDER,gender_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,GENDER_CONCEPT_ID,,,,,,,,No,
|
||||||
|
PROVIDER,gender_source_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,payer_plan_period_id,Yes,0,integer,0,,,Yes,0,Yes,0,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,person_id,Yes,0,integer,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,payer_plan_period_start_date,Yes,0,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,payer_plan_period_end_date,Yes,0,date,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,PAYER_PLAN_PERIOD,PAYER_PLAN_PERIOD_START_DATE,0,No,
|
||||||
|
PAYER_PLAN_PERIOD,payer_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,payer_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,PAYER_CONCEPT_ID,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,payer_source_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,plan_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,plan_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,PLAN_CONCEPT_ID,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,plan_source_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,sponsor_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,sponsor_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,SPONSOR_CONCEPT_ID,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,sponsor_source_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,family_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,0,,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,stop_reason_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,stop_reason_source_value,No,,varchar(50),0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,Yes,0,STOP_REASON_CONCEPT_ID,,,,,,,,No,
|
||||||
|
PAYER_PLAN_PERIOD,stop_reason_source_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,cost_id,Yes,0,INTEGER,0,,,Yes,0,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,cost_event_id,Yes,0,INTEGER,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,cost_domain_id,Yes,0,VARCHAR(20),0,,,No,,Yes,0,DOMAIN,DOMAIN_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,cost_type_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
COST,currency_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,total_charge,No,,FLOAT,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,total_cost,No,,FLOAT,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,total_paid,No,,FLOAT,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,paid_by_payer,No,,FLOAT,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,paid_by_patient,No,,FLOAT,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,paid_patient_copay,No,,FLOAT,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,paid_patient_coinsurance,No,,FLOAT,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,paid_patient_deductible,No,,FLOAT,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,paid_by_primary,No,,FLOAT,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,paid_ingredient_cost,No,,FLOAT,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,paid_dispensing_fee,No,,FLOAT,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,payer_plan_period_id,No,,INTEGER,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,amount_allowed,No,,FLOAT,0,,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,revenue_code_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,revenue_code_source_value,No,,VARCHAR(50),0,Revenue codes are a method to charge for a class of procedures and conditions in the U.S. hospital system.,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,drg_concept_id,No,,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
COST,drg_source_value,No,,VARCHAR(3),0,Diagnosis Related Groups are US codes used to classify hospital cases into one of approximately 500 groups. ,,No,,No,,,,,,,,No,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_ERA,drug_era_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_ERA,person_id,Yes,0,integer,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_ERA,drug_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Drug,0,Ingredient,0,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
DRUG_ERA,drug_era_start_date,Yes,0,datetime,0,,The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient. (NOT RIGHT),No,,No,,,,,,,,,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
DRUG_ERA,drug_era_end_date,Yes,0,datetime,0,,"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. (ARENT WE REQUIRING TO USE DRUG_EXPOSURE_END_DATE NOW????)",No,,No,,,,,,,,,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,DRUG_ERA,DRUG_ERA_START_DATE,0,No,
|
||||||
|
DRUG_ERA,drug_exposure_count,No,,integer,0,,,No,,No,,,,,,,,,,Yes,100,No,,No,,No,,,1,0,,,,,,No,
|
||||||
|
DRUG_ERA,gap_days,No,,integer,0,,"The Gap Days determine how many total drug-free days are observed between all Drug Exposure events that contribute to a DRUG_ERA record. It is assumed that the drugs are ""not stockpiled"" by the patient, i.e. that if a new drug prescription or refill is observed (a new DRUG_EXPOSURE record is written), the remaining supply from the previous events is abandoned. The difference between Persistence Window and Gap Days is that the former is the maximum drug-free time allowed between two subsequent DRUG_EXPOSURE records, while the latter is the sum of actual drug-free days for the given Drug Era under the above assumption of non-stockpiling.",No,,No,,,,,,,,,,Yes,100,No,,No,,No,,,0,0,,,,,,No,
|
||||||
|
DOSE_ERA,dose_era_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DOSE_ERA,person_id,Yes,0,integer,0,,,No,,Yes,0,PERSON,PERSON_ID,,,,,,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
DOSE_ERA,drug_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Drug,0,Ingredient,0,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
DOSE_ERA,unit_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Unit,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
DOSE_ERA,dose_value,Yes,0,float,0,,,No,,No,,,,,,,,,,Yes,100,No,,No,,No,,,0,0,,,,,,No,
|
||||||
|
DOSE_ERA,dose_era_start_date,Yes,0,datetime,0,,,No,,No,,,,,,,,,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
DOSE_ERA,dose_era_end_date,Yes,0,datetime,0,,,No,,No,,,,,,,,,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,No,
|
||||||
|
CONDITION_ERA,condition_era_id,Yes,0,integer,0,,,Yes,0,No,,,,,,,,,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_ERA,person_id,Yes,0,integer,0,,,No,,No,,PERSON,PERSON_ID,,,,,,,Yes,100,No,,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_ERA,condition_concept_id,Yes,0,integer,0,,,No,,Yes,0,CONCEPT,CONCEPT_ID,Condition,0,,,Yes,0,Yes,100,Yes,0,No,,No,,,,,,,,,,No,
|
||||||
|
CONDITION_ERA,condition_era_start_date,Yes,0,datetime,0,,,No,,No,,,,,,,,,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,Yes,0
|
||||||
|
CONDITION_ERA,condition_era_end_date,Yes,0,datetime,0,,,No,,No,,,,,,,,,,Yes,100,No,,No,,No,,,'1950-01-01',0,"DATEADD(dd,1,GETDATE())",0,PERSON,BIRTH_DATETIME,0,No,
|
||||||
|
CONDITION_ERA,condition_occurrence_count,No,,integer,0,,,No,,No,,,,,,,,,,Yes,100,No,,No,,No,,,1,0,,,,,,No,
|
||||||
|
|
|
@ -0,0 +1,23 @@
|
||||||
|
cdmTableName,schema,isRequired,conceptPrefix,measurePersonCompleteness,measurePersonCompletenessThreshold,validation,tableDescription,userGuidance,etlConventions
|
||||||
|
PERSON,CDM,Yes,,No,,,,,
|
||||||
|
OBSERVATION_PERIOD,CDM,Yes,,Yes,0,,,,
|
||||||
|
VISIT_OCCURRENCE,CDM,No,VISIT_,Yes,0,,,,
|
||||||
|
CONDITION_OCCURRENCE,CDM,No,CONDITION_,Yes,0,,,,
|
||||||
|
DRUG_EXPOSURE,CDM,No,DRUG_,Yes,0,,,,
|
||||||
|
PROCEDURE_OCCURRENCE,CDM,No,PROCEDURE_,Yes,0,,,,
|
||||||
|
DEVICE_EXPOSURE,CDM,No,DEVICE_,Yes,0,,,,
|
||||||
|
MEASUREMENT,CDM,No,MEASUREMENT_,Yes,0,,,,
|
||||||
|
VISIT_DETAIL,CDM,No,VISIT_DETAIL_,Yes,0,,,,
|
||||||
|
NOTE,CDM,No,,Yes,0,,,,
|
||||||
|
NOTE_NLP,CDM,No,,No,,,,,
|
||||||
|
OBSERVATION,CDM,No,OBSERVATION_,Yes,0,,,,
|
||||||
|
SPECIMEN,CDM,No,SPECIMEN_,Yes,0,,,,
|
||||||
|
FACT_RELATIONSHIP,CDM,No,,No,,,,,
|
||||||
|
LOCATION,CDM,No,,No,,,,,
|
||||||
|
CARE_SITE,CDM,No,,No,,,,,
|
||||||
|
PROVIDER,CDM,No,,No,,,,,
|
||||||
|
PAYER_PLAN_PERIOD,CDM,No,,Yes,0,,,,
|
||||||
|
COST,CDM,No,,No,,,,,
|
||||||
|
DRUG_ERA,CDM,No,,Yes,0,,,,
|
||||||
|
DOSE_ERA,CDM,No,,Yes,0,,,,
|
||||||
|
CONDITION_ERA,CDM,No,,Yes,0,,,,
|
||||||
|
Binary file not shown.
Binary file not shown.
|
|
@ -0,0 +1,22 @@
|
||||||
|
% Generated by roxygen2: do not edit by hand
|
||||||
|
% Please edit documentation in R/createDdlFromFile.R
|
||||||
|
\name{createDdlFromFile}
|
||||||
|
\alias{createDdlFromFile}
|
||||||
|
\title{Create a DDL script from a two csv files that detail the OMOP CDM Specifications. These files also form the basis of the CDM documentation and the Data Quality
|
||||||
|
Dashboard.}
|
||||||
|
\usage{
|
||||||
|
|
||||||
|
createDdlFromFile(cdmTableCsvLoc = "inst/csv/OMOP_CDMv5.3.1_Table_Level.csv",
|
||||||
|
cdmFieldCsvLoc = "inst/csv/OMOP_CDMv5.3.1_Field_Level.csv")
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{cdmTableCsvLoc}{The location of the csv file with the high-level CDM table information. This is defaulted to "inst/csv/OMOP_CDMv5.3.1_Table_Level.csv".
|
||||||
|
If a new version of this file was committed to the CDM repository the package automatically will grab it and place it in "inst/csv/".}
|
||||||
|
|
||||||
|
\item{cdmVersion}{The location of the csv file with the CDM field information. This is defaulted to "inst/csv/OMOP_CDMv5.3.1_Field_Level.csv".
|
||||||
|
If a new version of this file was committed to the CDM repository the package automatically will grab it and place it in "inst/csv/".}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Create a DDL script from a two csv files that detail the OMOP CDM Specifications. These files also form the basis of the CDM documentation and the Data Quality
|
||||||
|
Dashboard.
|
||||||
|
}
|
||||||
|
|
@ -1,428 +0,0 @@
|
||||||
"field","required","type","description","table"
|
|
||||||
"cohort_definition_id","Yes","INTEGER","A foreign key to a record in the COHORT_DEFINITION table containing relevant Cohort Definition information.","cohort"
|
|
||||||
"subject_id","Yes","INTEGER","A foreign key to the subject in the cohort. These could be referring to records in the PERSON, PROVIDER, VISIT_OCCURRENCE table.","cohort"
|
|
||||||
"cohort_start_date","Yes","DATE","The date when the Cohort Definition criteria for the Person, Provider or Visit first match.","cohort"
|
|
||||||
"cohort_end_date","Yes","DATE","The date when the Cohort Definition criteria for the Person, Provider or Visit no longer match or the Cohort membership was terminated.","cohort"
|
|
||||||
"cohort_definition_id","Yes","INTEGER","A unique identifier for each Cohort.","cohort_definition"
|
|
||||||
"cohort_definition_name","Yes","VARCHAR(255)","A short description of the Cohort.","cohort_definition"
|
|
||||||
"cohort_definition_description","No","VARCHAR(MAX)","A complete description of the Cohort definition","cohort_definition"
|
|
||||||
"definition_type_concept_id","Yes","INTEGER","Type defining what kind of Cohort Definition the record represents and how the syntax may be executed","cohort_definition"
|
|
||||||
"cohort_definition_syntax","No","VARCHAR(MAX)","Syntax or code to operationalize the Cohort definition","cohort_definition"
|
|
||||||
"subject_concept_id","Yes","INTEGER","A foreign key to the Concept to which defines the domain of subjects that are members of the cohort (e.g., Person, Provider, Visit).","cohort_definition"
|
|
||||||
"cohort_initiation_date","No","DATE","A date to indicate when the Cohort was initiated in the COHORT table","cohort_definition"
|
|
||||||
"condition_occurrence_id","Yes","BIGINT","A unique identifier for each Condition Occurrence event.","condition_occurrence"
|
|
||||||
"person_id","Yes","BIGINT","A foreign key identifier to the Person who is experiencing the condition. The demographic details of that Person are stored in the PERSON table.","condition_occurrence"
|
|
||||||
"condition_concept_id","Yes","INTEGER","A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies belonging to the 'Condition' domain.","condition_occurrence"
|
|
||||||
"condition_start_date","No","DATE","The date when the instance of the Condition is recorded.","condition_occurrence"
|
|
||||||
"condition_start_datetime","Yes","DATETIME","The date and time when the instance of the Condition is recorded.","condition_occurrence"
|
|
||||||
"condition_end_date","No","DATE","The date when the instance of the Condition is considered to have ended.","condition_occurrence"
|
|
||||||
"condition_end_datetime","No","DATETIME","The date when the instance of the Condition is considered to have ended.","condition_occurrence"
|
|
||||||
"condition_type_concept_id","Yes","INTEGER","A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the source data from which the Condition was recorded, the level of standardization, and the type of occurrence. These belong to the 'Condition Type' vocabulary","condition_occurrence"
|
|
||||||
"condition_status_concept_id","Yes","INTEGER","A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies reflecting the point of care at which the Condition was diagnosed.","condition_occurrence"
|
|
||||||
"stop_reason","No","VARCHAR(20)","The reason that the Condition was no longer present, as indicated in the source data.","condition_occurrence"
|
|
||||||
"provider_id","No","INTEGER","A foreign key to the Provider in the PROVIDER table who was responsible for capturing (diagnosing) the Condition.","condition_occurrence"
|
|
||||||
"visit_occurrence_id","No","INTEGER","A foreign key to the visit in the VISIT_OCCURRENCE table during which the Condition was determined (diagnosed).","condition_occurrence"
|
|
||||||
"visit_detail_id","No","INTEGER","A foreign key to the visit in the VISIT_DETAIL table during which the Condition was determined (diagnosed).","condition_occurrence"
|
|
||||||
"condition_source_value","No","VARCHAR(50)","The source code for the Condition 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.","condition_occurrence"
|
|
||||||
"condition_source_concept_id","Yes","INTEGER","A foreign key to a Condition Concept that refers to the code used in the source.","condition_occurrence"
|
|
||||||
"condition_status_source_value","No","VARCHAR(50)","The source code for the condition status as it appears in the source data. This code is mapped to a Standard Concept in the Standardized Vocabularies and the original code is stored here for reference.","condition_occurrence"
|
|
||||||
"device_exposure_id","Yes","BIGINT","A system-generated unique identifier for each Device Exposure.","device_exposure"
|
|
||||||
"person_id","Yes","BIGINT","A foreign key identifier to the Person who is subjected to the Device. The demographic details of that Person are stored in the PERSON table.","device_exposure"
|
|
||||||
"device_concept_id","Yes","INTEGER","A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies belonging to the 'Device' domain.","device_exposure"
|
|
||||||
"device_exposure_start_date","No","DATE","The date the Device or supply was applied or used.","device_exposure"
|
|
||||||
"device_exposure_start_datetime","Yes","DATETIME","The date and time the Device or supply was applied or used.","device_exposure"
|
|
||||||
"device_exposure_end_date","No","DATE","The date use of the Device or supply was ceased.","device_exposure"
|
|
||||||
"device_exposure_end_datetime","No","DATETIME","The date and time use of the Device or supply was ceased.","device_exposure"
|
|
||||||
"device_type_concept_id","Yes","INTEGER","A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the type of Device Exposure recorded. It indicates how the Device Exposure was represented in the source data and belongs to the 'Device Type' domain.","device_exposure"
|
|
||||||
"unique_device_id","No","VARCHAR(50)","A UDI or equivalent identifying the instance of the Device used in the Person.","device_exposure"
|
|
||||||
"quantity","No","INTEGER","The number of individual Devices used in the exposure.","device_exposure"
|
|
||||||
"provider_id","No","INTEGER","A foreign key to the provider in the PROVIDER table who initiated or administered the Device.","device_exposure"
|
|
||||||
"visit_occurrence_id","No","INTEGER","A foreign key to the visit in the VISIT_OCCURRENCE table during which the Device was used.","device_exposure"
|
|
||||||
"visit_detail_id","No","INTEGER","A foreign key to the visit detail record in the VISIT_DETAIL table during which the Device was used.","device_exposure"
|
|
||||||
"device_source_value","No","VARCHAR(50)","The source code for the Device as it appears in the source data. This code is mapped to a Standard Device Concept in the Standardized Vocabularies and the original code is stored here for reference.","device_exposure"
|
|
||||||
"device_source_concept_id","Yes","INTEGER","A foreign key to a Device Concept that refers to the code used in the source.","device_exposure"
|
|
||||||
"drug_exposure_id","Yes","BIGINT","A system-generated unique identifier for each Drug utilization event.","drug_exposure"
|
|
||||||
"person_id","Yes","BIGINT","A foreign key identifier to the Person who is subjected to the Drug. The demographic details of that Person are stored in the PERSON table.","drug_exposure"
|
|
||||||
"drug_concept_id","Yes","INTEGER","A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies belonging to the 'Drug' domain.","drug_exposure"
|
|
||||||
"drug_exposure_start_date","No","DATE","The start date for the current instance of Drug utilization. Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration procedure was recorded.","drug_exposure"
|
|
||||||
"drug_exposure_start_datetime","Yes","DATETIME","The start date and time for the current instance of Drug utilization. Valid entries include a start datetime of a prescription, the date and time a prescription was filled, or the date and time on which a Drug administration procedure was recorded.","drug_exposure"
|
|
||||||
"drug_exposure_end_date","No","DATE","The end date for the current instance of Drug utilization. Depending on different sources, it could be a known or an inferred date and denotes the last day at which the patient was still exposed to Drug.","drug_exposure"
|
|
||||||
"drug_exposure_end_datetime","No","DATETIME","The end date and time for the current instance of Drug utilization. Depending on different sources, it could be a known or an inferred date and time and denotes the last day at which the patient was still exposed to Drug.","drug_exposure"
|
|
||||||
"verbatim_end_date","No","DATE","The known end date of a drug_exposure as provided by the source.","drug_exposure"
|
|
||||||
"drug_type_concept_id","Yes","INTEGER","A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the type of Drug Exposure recorded. It indicates how the Drug Exposure was represented in the source data and belongs to the 'Drug Type' vocabulary.","drug_exposure"
|
|
||||||
"stop_reason","No","VARCHAR(20)","The reason the Drug was stopped. Reasons include regimen completed, changed, removed, etc.","drug_exposure"
|
|
||||||
"refills","No","INTEGER","The number of refills after the initial prescription. The initial prescription is not counted, values start with null.","drug_exposure"
|
|
||||||
"quantity","No","FLOAT","The quantity of drug as recorded in the original prescription or dispensing record.","drug_exposure"
|
|
||||||
"days_supply","No","INTEGER","The number of days of supply of the medication as prescribed. This reflects the intention of the provider for the length of exposure.","drug_exposure"
|
|
||||||
"sig","No","VARCHAR(MAX)","The directions ('signetur') on the Drug prescription as recorded in the original prescription (and printed on the container) or dispensing record.","drug_exposure"
|
|
||||||
"route_concept_id","Yes","INTEGER","A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies reflecting the route of administration and belonging to the 'Route' domain.","drug_exposure"
|
|
||||||
"lot_number","No","VARCHAR(50)","An identifier assigned to a particular quantity or lot of Drug product from the manufacturer.","drug_exposure"
|
|
||||||
"provider_id","No","INTEGER","A foreign key to the provider in the PROVIDER table who initiated (prescribed or administered) the Drug Exposure.","drug_exposure"
|
|
||||||
"visit_occurrence_id","No","INTEGER","A foreign key to the Visit in the VISIT_OCCURRENCE table during which the Drug Exposure was initiated.","drug_exposure"
|
|
||||||
"visit_detail_id","No","INTEGER","A foreign key to the Visit Detail in the VISIT_DETAIL table during which the Drug Exposure was initiated.","drug_exposure"
|
|
||||||
"drug_source_value","No","VARCHAR(50)","The source code for the Drug as it appears in the source data. This code is mapped to a Standard Drug concept in the Standardized Vocabularies and the original code is, stored here for reference.","drug_exposure"
|
|
||||||
"drug_source_concept_id","Yes","INTEGER","A foreign key to a Drug Concept that refers to the code used in the source.","drug_exposure"
|
|
||||||
"route_source_value","No","VARCHAR(50)","The information about the route of administration as detailed in the source.","drug_exposure"
|
|
||||||
"dose_unit_source_value","No","VARCHAR(50)","The information about the dose unit as detailed in the source.","drug_exposure"
|
|
||||||
"domain_concept_id_1","Yes","INTEGER","The concept representing the domain of fact one, from which the corresponding table can be inferred.","fact_relationship"
|
|
||||||
"fact_id_1","Yes","INTEGER","The unique identifier in the table corresponding to the domain of fact one.","fact_relationship"
|
|
||||||
"domain_concept_id_2","Yes","INTEGER","The concept representing the domain of fact two, from which the corresponding table can be inferred.","fact_relationship"
|
|
||||||
"fact_id_2","Yes","INTEGER","The unique identifier in the table corresponding to the domain of fact two.","fact_relationship"
|
|
||||||
"relationship_concept_id","Yes","INTEGER","A foreign key to a Standard Concept ID of relationship in the Standardized Vocabularies.","fact_relationship"
|
|
||||||
"measurement_id","Yes","INTEGER","A unique identifier for each Measurement.","measurement"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the Person about whom the measurement was recorded. The demographic details of that Person are stored in the PERSON table.","measurement"
|
|
||||||
"measurement_concept_id","Yes","INTEGER","A foreign key to the standard measurement concept identifier in the Standardized Vocabularies. These belong to the 'Measurement' domain, but could overlap with the 'Observation' domain (see #3 below).","measurement"
|
|
||||||
"measurement_date","No","DATE","The date of the Measurement.","measurement"
|
|
||||||
"measurement_datetime","Yes","DATETIME","The date and time of the Measurement. Some database systems don't have a datatype of time. To accommodate all temporal analyses, datatype datetime can be used (combining measurement_date and measurement_time [forum discussion](http://forums.ohdsi.org/t/date-time-and-datetime-problem-and-the-world-of-hours-and-1day/314))","measurement"
|
|
||||||
"measurement_time","No","VARCHAR(10)","The time of the Measurement. This is present for backwards compatibility and will be deprecated in an upcoming version","measurement"
|
|
||||||
"measurement_type_concept_id","Yes","INTEGER","A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the provenance from where the Measurement record was recorded. These belong to the 'Meas Type' vocabulary","measurement"
|
|
||||||
"operator_concept_id","No","INTEGER","A foreign key identifier to the predefined Concept in the Standardized Vocabularies reflecting the mathematical operator that is applied to the value_as_number. Operators are <, <=, =, >=, > and these concepts belong to the 'Meas Value Operator' domain.","measurement"
|
|
||||||
"value_as_number","No","FLOAT","A Measurement result where the result is expressed as a numeric value.","measurement"
|
|
||||||
"value_as_concept_id","No","INTEGER","A foreign key to a Measurement result represented as a Concept from the Standardized Vocabularies (e.g., positive/negative, present/absent, low/high, etc.). These belong to the 'Meas Value' domain","measurement"
|
|
||||||
"unit_concept_id","No","INTEGER","A foreign key to a Standard Concept ID of Measurement Units in the Standardized Vocabularies that belong to the 'Unit' domain.","measurement"
|
|
||||||
"range_low","No","FLOAT","The lower limit of the normal range of the Measurement result. The lower range is assumed to be of the same unit of measure as the Measurement value.","measurement"
|
|
||||||
"range_high","No","FLOAT","The upper limit of the normal range of the Measurement. The upper range is assumed to be of the same unit of measure as the Measurement value.","measurement"
|
|
||||||
"provider_id","No","INTEGER","A foreign key to the provider in the PROVIDER table who was responsible for initiating or obtaining the measurement.","measurement"
|
|
||||||
"visit_occurrence_id","No","INTEGER","A foreign key to the Visit in the VISIT_OCCURRENCE table during which the Measurement was recorded.","measurement"
|
|
||||||
"visit_detail_id","No","INTEGER","A foreign key to the Visit Detail in the VISIT_DETAIL table during which the Measurement was recorded.","measurement"
|
|
||||||
"measurement_source_value","No","VARCHAR(50)","The Measurement name as it appears in the source data. This code is mapped to a Standard Concept in the Standardized Vocabularies and the original code is stored here for reference.","measurement"
|
|
||||||
"measurement_source_concept_id","Yes","INTEGER","A foreign key to a Concept in the Standard Vocabularies that refers to the code used in the source.","measurement"
|
|
||||||
"unit_source_value","No","VARCHAR(50)","The source code for the unit as it appears in the source data. This code is mapped to a standard unit concept in the Standardized Vocabularies and the original code is stored here for reference.","measurement"
|
|
||||||
"value_source_value","No","VARCHAR(50)","The source value associated with the content of the value_as_number or value_as_concept_id as stored in the source data.","measurement"
|
|
||||||
"note_id","Yes","INTEGER","A unique identifier for each note.","note"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the Person about whom the Note was recorded. The demographic details of that Person are stored in the PERSON table.","note"
|
|
||||||
"note_event_id","No","INTEGER","A foreign key identifier to the event (e.g. Measurement, Procedure, Visit, Drug Exposure, etc) record during which the note was recorded.","note"
|
|
||||||
"note_event_field_concept_id","No","INTEGER","A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the field to which the note_event_id is referring.","note"
|
|
||||||
"note_date","No","DATE","The date the note was recorded.","note"
|
|
||||||
"note_datetime","Yes","DATETIME","The date and time the note was recorded.","note"
|
|
||||||
"note_type_concept_id","Yes","INTEGER","A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the type, origin or provenance of the Note. These belong to the 'Note Type' vocabulary","note"
|
|
||||||
"note_class_concept_id","Yes","INTEGER","A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the HL7 LOINC Document Type Vocabulary classification of the note.","note"
|
|
||||||
"note_title","No","VARCHAR(250)","The title of the Note as it appears in the source.","note"
|
|
||||||
"note_text","Yes","VARCHAR(MAX)","The content of the Note.","note"
|
|
||||||
"encoding_concept_id","Yes","INTEGER","A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the note character encoding type","note"
|
|
||||||
"language_concept_id","Yes","INTEGER","A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the language of the note","note"
|
|
||||||
"provider_id","No","INTEGER","A foreign key to the Provider in the PROVIDER table who took the Note.","note"
|
|
||||||
"visit_occurrence_id","No","INTEGER","A foreign key to the Visit in the VISIT_OCCURRENCE table when the Note was taken.","note"
|
|
||||||
"visit_detail_id","No","INTEGER","A foreign key to the Visit in the VISIT_DETAIL table when the Note was taken.","note"
|
|
||||||
"note_source_value","No","VARCHAR(50)","The source value associated with the origin of the Note","note"
|
|
||||||
"note_nlp_id","Yes","INTEGER","A unique identifier for each term extracted from a note.","note_nlp"
|
|
||||||
"note_id","Yes","INTEGER","A foreign key to the Note table note the term was","note_nlp"
|
|
||||||
"section_concept_id","Yes","INTEGER","A foreign key to the predefined Concept in the Standardized Vocabularies representing the section of the extracted term.","note_nlp"
|
|
||||||
"snippet","No","VARCHAR(250)","A small window of text surrounding the term.","note_nlp"
|
|
||||||
"offset","No","VARCHAR(50)","Character offset of the extracted term in the input note.","note_nlp"
|
|
||||||
"lexical_variant","Yes","VARCHAR(250)","Raw text extracted from the NLP tool.","note_nlp"
|
|
||||||
"note_nlp_concept_id","Yes","INTEGER","A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the normalized concept for the extracted term. Domain of the term is represented as part of the Concept table.","note_nlp"
|
|
||||||
"note_nlp_source_concept_id","Yes","INTEGER","A foreign key to a Concept that refers to the code in the source vocabulary used by the NLP system","note_nlp"
|
|
||||||
"nlp_system","No","VARCHAR(250)","Name and version of the NLP system that extracted the term.Useful for data provenance.","note_nlp"
|
|
||||||
"nlp_date","Yes","DATE","The date of the note processing.Useful for data provenance.","note_nlp"
|
|
||||||
"nlp_datetime","No","DATETIME","The date and time of the note processing. Useful for data provenance.","note_nlp"
|
|
||||||
"term_exists","No","VARCHAR(1)","A summary modifier that signifies presence or absence of the term for a given patient. Useful for quick querying.","note_nlp"
|
|
||||||
"term_temporal","No","VARCHAR(50)","An optional time modifier associated with the extracted term. (for now “pastâ€<C3A2> or “presentâ€<C3A2> only). Standardize it later.","note_nlp"
|
|
||||||
"term_modifiers","No","VARCHAR(2000)","A compact description of all the modifiers of the specific term extracted by the NLP system. (e.g. “son has rashâ€<C3A2> ? “negated=no,subject=family, certainty=undef,conditional=false,general=falseâ€<C3A2>).","note_nlp"
|
|
||||||
"observation_id","Yes","INTEGER","A unique identifier for each observation.","observation"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the Person about whom the observation was recorded. The demographic details of that Person are stored in the PERSON table.","observation"
|
|
||||||
"observation_concept_id","Yes","INTEGER","A foreign key to the standard observation concept identifier in the Standardized Vocabularies.","observation"
|
|
||||||
"observation_date","No","DATE","The date of the observation.","observation"
|
|
||||||
"observation_datetime","Yes","DATETIME","The date and time of the observation.","observation"
|
|
||||||
"observation_type_concept_id","Yes","INTEGER","A foreign key to the predefined concept identifier in the Standardized Vocabularies reflecting the type of the observation.","observation"
|
|
||||||
"value_as_number","No","FLOAT","The observation result stored as a number. This is applicable to observations where the result is expressed as a numeric value.","observation"
|
|
||||||
"value_as_string","No","VARCHAR(60)","The observation result stored as a string. This is applicable to observations where the result is expressed as verbatim text.","observation"
|
|
||||||
"value_as_concept_id","No","INTEGER","A foreign key to an observation result stored as a Concept ID. This is applicable to observations where the result can be expressed as a Standard Concept from the Standardized Vocabularies (e.g., positive/negative, present/absent, low/high, etc.).","observation"
|
|
||||||
"qualifier_concept_id","No","INTEGER","A foreign key to a Standard Concept ID for a qualifier (e.g., severity of drug-drug interaction alert)","observation"
|
|
||||||
"unit_concept_id","No","INTEGER","A foreign key to a Standard Concept ID of measurement units in the Standardized Vocabularies.","observation"
|
|
||||||
"provider_id","No","INTEGER","A foreign key to the provider in the PROVIDER table who was responsible for making the observation.","observation"
|
|
||||||
"visit_occurrence_id","No","INTEGER","A foreign key to the visit in the VISIT_OCCURRENCE table during which the observation was recorded.","observation"
|
|
||||||
"visit_detail_id","No","INTEGER","A foreign key to the visit in the VISIT_DETAIL table during which the observation was recorded.","observation"
|
|
||||||
"observation_source_value","No","VARCHAR(50)","The observation code as it appears in the source data. This code is mapped to a Standard Concept in the Standardized Vocabularies and the original code is, stored here for reference.","observation"
|
|
||||||
"observation_source_concept_id","Yes","INTEGER","A foreign key to a Concept that refers to the code used in the source.","observation"
|
|
||||||
"unit_source_value","No","VARCHAR(50)","The source code for the unit as it appears in the source data. This code is mapped to a standard unit concept in the Standardized Vocabularies and the original code is, stored here for reference.","observation"
|
|
||||||
"qualifier_source_value","No","VARCHAR(50)","The source value associated with a qualifier to characterize the observation","observation"
|
|
||||||
"observation_event_id","No","INTEGER","A foreign key to an event table (e.g., PROCEDURE_OCCURRENCE_ID).","observation"
|
|
||||||
"obs_event_field_concept_id","Yes","INTEGER","A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies referring to the field represented in the OBSERVATION_EVENT_ID.","observation"
|
|
||||||
"value_as_datetime","No","INTEGER","The observation result stored as a datetime value. This is applicable to observations where the result is expressed as a point in time.","observation"
|
|
||||||
"observation_period_id","Yes","INTEGER","A unique identifier for each observation period.","observation_period"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the person for whom the observation period is defined. The demographic details of that person are stored in the person table.","observation_period"
|
|
||||||
"observation_period_start_date","Yes","DATE","The start date of the observation period for which data are available from the data source.","observation_period"
|
|
||||||
"observation_period_end_date","Yes","DATE","The end date of the observation period for which data are available from the data source.","observation_period"
|
|
||||||
"period_type_concept_id","Yes","INTEGER","A foreign key identifier to the predefined concept in the Standardized Vocabularies reflecting the source of the observation period information, belonging to the 'Obs Period Type' vocabulary","observation_period"
|
|
||||||
"person_id","Yes","INTEGER","A unique identifier for each person.","person"
|
|
||||||
"gender_concept_id","Yes","INTEGER","A foreign key that refers to an identifier in the CONCEPT table for the unique gender of the person.","person"
|
|
||||||
"year_of_birth","Yes","INTEGER","The year of birth of the person. For data sources with date of birth, the year is extracted. For data sources where the year of birth is not available, the approximate year of birth is derived based on any age group categorization available.","person"
|
|
||||||
"month_of_birth","No","INTEGER","The month of birth of the person. For data sources that provide the precise date of birth, the month is extracted and stored in this field.","person"
|
|
||||||
"day_of_birth","No","INTEGER","The day of the month of birth of the person. For data sources that provide the precise date of birth, the day is extracted and stored in this field.","person"
|
|
||||||
"birth_datetime","No","DATETIME","The date and time of birth of the person.","person"
|
|
||||||
"death_datetime","No","DATETIME","The date and time of death of the person.","person"
|
|
||||||
"race_concept_id","Yes","INTEGER","A foreign key that refers to an identifier in the CONCEPT table for the unique race of the person, belonging to the 'Race' vocabulary.","person"
|
|
||||||
"ethnicity_concept_id","Yes","INTEGER","A foreign key that refers to the standard concept identifier in the Standardized Vocabularies for the ethnicity of the person, belonging to the 'Ethnicity' vocabulary.","person"
|
|
||||||
"location_id","No","INTEGER","A foreign key to the place of residency for the person in the location table, where the detailed address information is stored.","person"
|
|
||||||
"provider_id","No","INTEGER","A foreign key to the primary care provider the person is seeing in the provider table.","person"
|
|
||||||
"care_site_id","No","INTEGER","A foreign key to the site of primary care in the care_site table, where the details of the care site are stored.","person"
|
|
||||||
"person_source_value","No","VARCHAR(50)","An (encrypted) key derived from the person identifier in the source data. This is necessary when a use case requires a link back to the person data at the source dataset.","person"
|
|
||||||
"gender_source_value","No","VARCHAR(50)","The source code for the gender of the person as it appears in the source data. The person’s gender is mapped to a standard gender concept in the Standardized Vocabularies; the original value is stored here for reference.","person"
|
|
||||||
"gender_source_concept_id","Yes","INTEGER","A foreign key to the gender concept that refers to the code used in the source.","person"
|
|
||||||
"race_source_value","No","VARCHAR(50)","The source code for the race of the person as it appears in the source data. The person race is mapped to a standard race concept in the Standardized Vocabularies and the original value is stored here for reference.","person"
|
|
||||||
"race_source_concept_id","Yes","INTEGER","A foreign key to the race concept that refers to the code used in the source.","person"
|
|
||||||
"ethnicity_source_value","No","VARCHAR(50)","The source code for the ethnicity of the person as it appears in the source data. The person ethnicity is mapped to a standard ethnicity concept in the Standardized Vocabularies and the original code is, stored here for reference.","person"
|
|
||||||
"ethnicity_source_concept_id","Yes","INTEGER","A foreign key to the ethnicity concept that refers to the code used in the source.","person"
|
|
||||||
"procedure_occurrence_id","Yes","INTEGER","A system-generated unique identifier for each Procedure Occurrence.","procedure_occurrence"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the Person who is subjected to the Procedure. The demographic details of that Person are stored in the PERSON table.","procedure_occurrence"
|
|
||||||
"procedure_concept_id","Yes","INTEGER","A foreign key that refers to a standard procedure Concept identifier in the Standardized Vocabularies.","procedure_occurrence"
|
|
||||||
"procedure_date","No","DATE","The date on which the Procedure was performed.","procedure_occurrence"
|
|
||||||
"procedure_datetime","Yes","DATETIME","The date and time on which the Procedure was performed.","procedure_occurrence"
|
|
||||||
"procedure_type_concept_id","Yes","INTEGER","A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the type of source data from which the procedure record is derived, belonging to the 'Procedure Type' vocabulary.","procedure_occurrence"
|
|
||||||
"modifier_concept_id","Yes","INTEGER","A foreign key to a Standard Concept identifier for a modifier to the Procedure (e.g. bilateral). These concepts are typically distinguished by 'Modifier' concept classes (e.g., 'CPT4 Modifier' as part of the 'CPT4' vocabulary).","procedure_occurrence"
|
|
||||||
"quantity","No","INTEGER","The quantity of procedures ordered or administered.","procedure_occurrence"
|
|
||||||
"provider_id","No","INTEGER","A foreign key to the provider in the PROVIDER table who was responsible for carrying out the procedure.","procedure_occurrence"
|
|
||||||
"visit_occurrence_id","No","INTEGER","A foreign key to the Visit in the VISIT_OCCURRENCE table during which the Procedure was carried out.","procedure_occurrence"
|
|
||||||
"visit_detail_id","No","INTEGER","A foreign key to the Visit Detail in the VISIT_DETAIL table during which the Procedure was carried out.","procedure_occurrence"
|
|
||||||
"procedure_source_value","No","VARCHAR(50)","The source code for the Procedure as it appears in the source data. This code is mapped to a standard procedure Concept in the Standardized Vocabularies and the original code is, stored here for reference. Procedure source codes are typically ICD-9-Proc, CPT-4, HCPCS or OPCS-4 codes.","procedure_occurrence"
|
|
||||||
"procedure_source_concept_id","Yes","INTEGER","A foreign key to a Procedure Concept that refers to the code used in the source.","procedure_occurrence"
|
|
||||||
"modifier_source_value","No","VARCHAR(50)","The source code for the qualifier as it appears in the source data.","procedure_occurrence"
|
|
||||||
"specimen_id","Yes","INTEGER","A unique identifier for each specimen.","specimen"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the Person for whom the Specimen is recorded.","specimen"
|
|
||||||
"specimen_concept_id","Yes","INTEGER","A foreign key referring to a Standard Concept identifier in the Standardized Vocabularies for the Specimen.","specimen"
|
|
||||||
"specimen_type_concept_id","Yes","INTEGER","A foreign key referring to the Concept identifier in the Standardized Vocabularies reflecting the system of record from which the Specimen was represented in the source data.","specimen"
|
|
||||||
"specimen_date","No","DATE","The date the specimen was obtained from the Person.","specimen"
|
|
||||||
"specimen_datetime","Yes","DATETIME","The date and time on the date when the Specimen was obtained from the person.","specimen"
|
|
||||||
"quantity","No","FLOAT","The amount of specimen collection from the person during the sampling procedure.","specimen"
|
|
||||||
"unit_concept_id","No","INTEGER","A foreign key to a Standard Concept identifier for the Unit associated with the numeric quantity of the Specimen collection.","specimen"
|
|
||||||
"anatomic_site_concept_id","Yes","INTEGER","A foreign key to a Standard Concept identifier for the anatomic location of specimen collection.","specimen"
|
|
||||||
"disease_status_concept_id","Yes","INTEGER","A foreign key to a Standard Concept identifier for the Disease Status of specimen collection.","specimen"
|
|
||||||
"specimen_source_id","No","VARCHAR(50)","The Specimen identifier as it appears in the source data.","specimen"
|
|
||||||
"specimen_source_value","No","VARCHAR(50)","The Specimen value as it appears in the source data. This value is mapped to a Standard Concept in the Standardized Vocabularies and the original code is, stored here for reference.","specimen"
|
|
||||||
"unit_source_value","No","VARCHAR(50)","The information about the Unit as detailed in the source.","specimen"
|
|
||||||
"anatomic_site_source_value","No","VARCHAR(50)","The information about the anatomic site as detailed in the source.","specimen"
|
|
||||||
"disease_status_source_value","No","VARCHAR(50)","The information about the disease status as detailed in the source.","specimen"
|
|
||||||
"survey_conduct_id","Yes","INTEGER","Unique identifier for each completed survey.","survey_conduct"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the Person in the PERSON table about whom the survey was completed.","survey_conduct"
|
|
||||||
"survey_concept_id","Yes","INTEGER","A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the name and identity of the survey.","survey_conduct"
|
|
||||||
"survey_start_date","No","DATE","Date on which the survey was started.","survey_conduct"
|
|
||||||
"survey_start_datetime","No","DATETIME","Date and time the survey was started.","survey_conduct"
|
|
||||||
"survey_end_date","Yes","DATE","Date on which the survey was completed.","survey_conduct"
|
|
||||||
"survey_end_datetime","No","DATETIME","Date and time the survey was completed.","survey_conduct"
|
|
||||||
"provider_id","NoÂ","INTEGERÂ","A foreign key to the provider in the provider table who was associated with the survey completion.","survey_conduct"
|
|
||||||
"assisted_concept_id","Yes","INTEGER","A foreign key to the predefined Concept identifier in the Standardized Vocabularies indicating whether the survey was completed with assistance.","survey_conduct"
|
|
||||||
"respondent_type_concept_id","Yes","INTEGER","A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the respondent type. Example: Research Associate, Patient.","survey_conduct"
|
|
||||||
"timing_concept_id","Yes","INTEGER","A foreign key to the predefined Concept identifier in the Standardized Vocabularies that refers to a certain timing. Example: 3 month follow-up, 6 month follow-up.","survey_conduct"
|
|
||||||
"collection_method_concept_id","Yes","INTEGER","A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the data collection method (e.g. Paper, Telephone, Electronic Questionnaire).","survey_conduct"
|
|
||||||
"assisted_source_value","No","VARCHAR(50)","Source value representing whether patient required assistance to complete the survey. Example: “Completed without assistanceâ€<C3A2>, â€<C3A2>Completed with assistanceâ€<C3A2>.","survey_conduct"
|
|
||||||
"respondent_type_source_value","No","VARCHAR(100)","Source code representing role of person who completed the survey.","survey_conduct"
|
|
||||||
"timing_source_value","No","VARCHAR(100)","Text string representing the timing of the survey. Example: Baseline, 6-month follow-up.","survey_conduct"
|
|
||||||
"collection_method_source_value","No","VARCHAR(100)","The collection method as it appears in the source data.","survey_conduct"
|
|
||||||
"survey_source_value","No","VARCHAR(100)","The survey name/title as it appears in the source data.","survey_conduct"
|
|
||||||
"survey_source_concept_id","Yes","INTEGER","A foreign key to a predefined Concept that refers to the code for the survey name/title used in the source.","survey_conduct"
|
|
||||||
"survey_source_identifier","No","VARCHAR(100)","Unique identifier for each completed survey in source system.","survey_conduct"
|
|
||||||
"validated_survey_concept_id","Yes","INTEGER","A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the validation status of the survey.","survey_conduct"
|
|
||||||
"validated_survey_source_value","No","INTEGER","Source value representing the validation status of the survey.","survey_conduct"
|
|
||||||
"survey_version_number","No","VARCHAR(20)","Version number of the questionnaire or survey used.","survey_conduct"
|
|
||||||
"visit_occurrence_id","No","INTEGER","A foreign key to the VISIT_OCCURRENCE table during which the survey was completed","survey_conduct"
|
|
||||||
"response_visit_occurrence_id","No","INTEGERÂ","A foreign key to the visit in the VISIT_OCCURRENCE table during which treatment was carried out that relates to this survey.","survey_conduct"
|
|
||||||
"visit_detail_id","Yes","INTEGER","A unique identifier for each Person's visit or encounter at a healthcare provider.","visit_detail"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the Person for whom the visit is recorded. The demographic details of that Person are stored in the PERSON table.","visit_detail"
|
|
||||||
"visit_detail_concept_id","Yes","INTEGER","A foreign key that refers to a visit Concept identifier in the Standardized Vocabularies belonging to the 'Visit' Vocabulary.","visit_detail"
|
|
||||||
"visit_detail_start_date","No","DATE","The start date of the visit.","visit_detail"
|
|
||||||
"visit_detail_start_datetime","Yes","DATETIME","The date and time of the visit started.","visit_detail"
|
|
||||||
"visit_detail_end_date","No","DATE","The end date of the visit. If this is a one-day visit the end date should match the start date.","visit_detail"
|
|
||||||
"visit_detail_end_datetime","Yes","DATETIME","The date and time of the visit end.","visit_detail"
|
|
||||||
"visit_detail_type_concept_id","Yes","INTEGER","A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the type of source data from which the visit record is derived belonging to the 'Visit Type' vocabulary.","visit_detail"
|
|
||||||
"provider_id","No","INTEGER","A foreign key to the provider in the provider table who was associated with the visit.","visit_detail"
|
|
||||||
"care_site_id","No","INTEGER","A foreign key to the care site in the care site table that was visited.","visit_detail"
|
|
||||||
"visit_detail_source_value","No","STRING(50)","The source code for the visit as it appears in the source data.","visit_detail"
|
|
||||||
"visit_detail_source_concept_id","Yes","INTEGER","A foreign key to a Concept that refers to the code used in the source.","visit_detail"
|
|
||||||
"admitted_from_source_value","No","VARCHAR(50)","The source code for the admitting source as it appears in the source data.","visit_detail"
|
|
||||||
"admitted_from_concept_id","Yes","INTEGER","A foreign key to the predefined concept in the 'Place of Service' Vocabulary reflecting the admitting source for a visit.","visit_detail"
|
|
||||||
"discharge_to_source_value","No","VARCHAR(50)","The source code for the discharge disposition as it appears in the source data.","visit_detail"
|
|
||||||
"discharge_to_concept_id","Yes","INTEGER","A foreign key to the predefined concept in the 'Place of Service' Vocabulary reflecting the discharge disposition for a visit.","visit_detail"
|
|
||||||
"preceding_visit_detail_id","No","INTEGER","A foreign key to the VISIT_DETAIL table of the visit immediately preceding this visit","visit_detail"
|
|
||||||
"visit_detail_parent_id","No","INTEGER","A foreign key to the VISIT_DETAIL table record to represent the immediate parent visit-detail record.","visit_detail"
|
|
||||||
"visit_occurrence_id","Yes","INTEGER","A foreign key that refers to the record in the VISIT_OCCURRENCE table. This is a required field, because for every visit_detail is a child of visit_occurrence and cannot exist without a corresponding parent record in visit_occurrence.","visit_detail"
|
|
||||||
"visit_occurrence_id","Yes","INTEGER","A unique identifier for each Person's visit or encounter at a healthcare provider.","visit_occurrence"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the Person for whom the visit is recorded. The demographic details of that Person are stored in the PERSON table.","visit_occurrence"
|
|
||||||
"visit_concept_id","Yes","INTEGER","A foreign key that refers to a visit Concept identifier in the Standardized Vocabularies belonging to the 'Visit' Vocabulary.","visit_occurrence"
|
|
||||||
"visit_start_date","No","DATE","The start date of the visit.","visit_occurrence"
|
|
||||||
"visit_start_datetime","Yes","DATETIME","The date and time of the visit started.","visit_occurrence"
|
|
||||||
"visit_end_date","No","DATE","The end date of the visit. If this is a one-day visit the end date should match the start date.","visit_occurrence"
|
|
||||||
"visit_end_datetime","Yes","DATETIME","The date and time of the visit end.","visit_occurrence"
|
|
||||||
"visit_type_concept_id","Yes","INTEGER","A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the type of source data from which the visit record is derived belonging to the 'Visit Type' vocabulary.","visit_occurrence"
|
|
||||||
"provider_id","No","INTEGER","A foreign key to the provider in the provider table who was associated with the visit.","visit_occurrence"
|
|
||||||
"care_site_id","No","INTEGER","A foreign key to the care site in the care site table that was visited.","visit_occurrence"
|
|
||||||
"visit_source_value","No","VARCHAR(50)","The source code for the visit as it appears in the source data.","visit_occurrence"
|
|
||||||
"visit_source_concept_id","Yes","INTEGER","A foreign key to a Concept that refers to the code used in the source.","visit_occurrence"
|
|
||||||
"admitting_source_concept_id","Yes","INTEGER","A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the admitting source for a visit.","visit_occurrence"
|
|
||||||
"admitting_source_value","No","VARCHAR(50)","The source code for the admitting source as it appears in the source data.","visit_occurrence"
|
|
||||||
"discharge_to_concept_id","Yes","INTEGER","A foreign key to the predefined concept in the Place of Service Vocabulary reflecting the discharge disposition for a visit.","visit_occurrence"
|
|
||||||
"discharge_to_source_value","No","VARCHAR(50)","The source code for the discharge disposition as it appears in the source data.","visit_occurrence"
|
|
||||||
"preceding_visit_occurrence_id","No","INTEGER","A foreign key to the VISIT_OCCURRENCE table of the visit immediately preceding this visit","visit_occurrence"
|
|
||||||
"condition_era_id","Yes","INTEGER","A unique identifier for each Condition Era.","condition_era"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the Person who is experiencing the Condition during the Condition Era. The demographic details of that Person are stored in the PERSON table.","condition_era"
|
|
||||||
"condition_concept_id","Yes","INTEGER","A foreign key that refers to a standard Condition Concept identifier in the Standardized Vocabularies.","condition_era"
|
|
||||||
"condition_era_start_datetime","Yes","DATE","The start date for the Condition Era constructed from the individual instances of Condition Occurrences. It is the start date of the very first chronologically recorded instance of the condition.","condition_era"
|
|
||||||
"condition_era_end_datetime","Yes","DATE","The end date for the Condition Era constructed from the individual instances of Condition Occurrences. It is the end date of the final continuously recorded instance of the Condition.","condition_era"
|
|
||||||
"condition_occurrence_count","No","INTEGER","The number of individual Condition Occurrences used to construct the condition era.","condition_era"
|
|
||||||
"dose_era_id","Yes","INTEGER","A unique identifier for each Dose Era.","dose_era"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the Person who is subjected to the drug during the drug era. The demographic details of that Person are stored in the PERSON table.","dose_era"
|
|
||||||
"drug_concept_id","Yes","INTEGER","A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies for the active Ingredient Concept.","dose_era"
|
|
||||||
"unit_concept_id","Yes","INTEGER","A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies for the unit concept.","dose_era"
|
|
||||||
"dose_value","Yes","FLOAT","The numeric value of the dose.","dose_era"
|
|
||||||
"dose_era_start_datetime","Yes","DATE","The start date for the drug era constructed from the individual instances of drug exposures. It is the start date of the very first chronologically recorded instance of utilization of a drug.","dose_era"
|
|
||||||
"dose_era_end_datetime","Yes","DATE","The end date for the drug era constructed from the individual instance of drug exposures. It is the end date of the final continuously recorded instance of utilization of a drug.","dose_era"
|
|
||||||
"drug_era_id","Yes","INTEGER","A unique identifier for each Drug Era.","drug_era"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the Person who is subjected to the Drug during the fDrug Era. The demographic details of that Person are stored in the PERSON table.","drug_era"
|
|
||||||
"drug_concept_id","Yes","INTEGER","A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies for the Ingredient Concept.","drug_era"
|
|
||||||
"drug_era_start_datetime","Yes","DATE","The start date for the Drug Era constructed from the individual instances of Drug Exposures. It is the start date of the very first chronologically recorded instance of conutilization of a Drug.","drug_era"
|
|
||||||
"drug_era_end_datetime","Yes","DATE","The end date for the drug era constructed from the individual instance of drug exposures. It is the end date of the final continuously recorded instance of utilization of a drug.","drug_era"
|
|
||||||
"drug_exposure_count","No","INTEGER","The number of individual Drug Exposure occurrences used to construct the Drug Era.","drug_era"
|
|
||||||
"gap_days","No","INTEGER","The number of days that are not covered by DRUG_EXPOSURE records that were used to make up the era record.","drug_era"
|
|
||||||
"cost_id","Yes","INTEGER","A unique identifier for each COST record.","cost"
|
|
||||||
"person_id","Yes","INTEGER","A unique identifier for each PERSON.","cost"
|
|
||||||
"cost_event_id","Yes","INTEGER","A foreign key identifier to the event (e.g. Measurement, Procedure, Visit, Drug Exposure, etc) record for which cost data are recorded.","cost"
|
|
||||||
"cost_event_field_concept_id","Yes","INTEGER","A foreign key identifier to a concept in the CONCEPT table representing the identity of the field represented by COST_EVENT_ID","cost"
|
|
||||||
"cost_concept_id","Yes","INTEGER","A foreign key that refers to a Standard Cost Concept identifier in the Standardized Vocabularies belonging to the 'Cost' vocabulary.","cost"
|
|
||||||
"cost_type_concept_id","Yes","INTEGER","A foreign key identifier to a concept in the CONCEPT table for the provenance or the source of the COST data and belonging to the 'Cost Type' vocabulary","cost"
|
|
||||||
"cost_source_concept_id","Yes","INTEGER","A foreign key to a Cost Concept that refers to the code used in the source.","cost"
|
|
||||||
"cost_source_value","No","VARCHAR(50)","The source value for the cost as it appears in the source data","cost"
|
|
||||||
"currency_concept_id","Yes","INTEGER","A foreign key identifier to the concept representing the 3-letter code used to delineate international currencies, such as USD for US Dollar. These belong to the 'Currency' vocabulary","cost"
|
|
||||||
"cost","Yes","FLOAT","The actual financial cost amount","cost"
|
|
||||||
"incurred_date","Yes","DATE","The first date of service of the clinical event corresponding to the cost as in table capturing the information (e.g. date of visit, date of procedure, date of condition, date of drug etc).","cost"
|
|
||||||
"billed_date","No","DATE","The date a bill was generated for a service or encounter","cost"
|
|
||||||
"paid_date","No","DATE","The date payment was received for a service or encounter","cost"
|
|
||||||
"revenue_code_concept_id","Yes","INTEGER","A foreign key referring to a Standard Concept ID in the Standardized Vocabularies for Revenue codes belonging to the 'Revenue Code' vocabulary.","cost"
|
|
||||||
"drg_concept_id","Yes","INTEGER","A foreign key referring to a Standard Concept ID in the Standardized Vocabularies for DRG codes belonging to the 'DRG' vocabulary.","cost"
|
|
||||||
"revenue_code_source_value","No","VARCHAR(50)","The source value for the Revenue code as it appears in the source data, stored here for reference.","cost"
|
|
||||||
"drg_source_value","No","VARCHAR(50)","The source value for the 3-digit DRG source code as it appears in the source data, stored here for reference.","cost"
|
|
||||||
"payer_plan_period_id","No","INTEGER","A foreign key to the PAYER_PLAN_PERIOD table, where the details of the Payer, Plan and Family are stored. Record the payer_plan_id that relates to the payer who contributed to the paid_by_payer field.","cost"
|
|
||||||
"payer_plan_period_id","Yes","INTEGER","A identifier for each unique combination of payer, plan, family code and time span.","payer_plan_period"
|
|
||||||
"person_id","Yes","INTEGER","A foreign key identifier to the Person covered by the payer. The demographic details of that Person are stored in the PERSON table.","payer_plan_period"
|
|
||||||
"contract_person_id","No","INTEGER","A foreign key identifier to the person_id in person table, for the person who is the primary subscriber/contract owner for the record in the payer_plan_period table. Maybe the same person or different person, depending on who is the primary subscriber/contract owner.","payer_plan_period"
|
|
||||||
"payer_plan_period_start_date","Yes","DATE","The start date of the payer plan period.","payer_plan_period"
|
|
||||||
"payer_plan_period_end_date","Yes","DATE","The end date of the payer plan period.","payer_plan_period"
|
|
||||||
"payer_concept_id","Yes","INTEGER","A foreign key that refers to a standard Payer concept identifier in the Standarized Vocabularies","payer_plan_period"
|
|
||||||
"payer_source_value","No","VARCHAR(50)","The source code for the payer as it appears in the source data.","payer_plan_period"
|
|
||||||
"payer_source_concept_id","Yes","INTEGER","A foreign key to a payer concept that refers to the code used in the source.","payer_plan_period"
|
|
||||||
"plan_concept_id","Yes","INTEGER","A foreign key that refers to a standard plan concept identifier that represents the health benefit plan in the Standardized Vocabularies.","payer_plan_period"
|
|
||||||
"plan_source_value","No","VARCHAR(50)","The source code for the Person's health benefit plan as it appears in the source data.","payer_plan_period"
|
|
||||||
"plan_source_concept_id","Yes","INTEGER","A foreign key to a plan concept that refers to the plan code used in the source data.","payer_plan_period"
|
|
||||||
"contract_concept_id","Yes","INTEGER","A foreign key to a standard concept representing the reason justifying the contract between person_id and contract_person_id.","payer_plan_period"
|
|
||||||
"contract_source_value","No","INTEGER","The source code representing the reason justifying the contract. Usually it is family relationship like a spouse, domestic partner, child etc.","payer_plan_period"
|
|
||||||
"contract_source_concept_id","Yes","INTEGER","A foreign key to a concept that refers to the code used in the source as the reason justifying the contract.","payer_plan_period"
|
|
||||||
"sponsor_concept_id","Yes","INTEGER","A foreign key that refers to a concept identifier that represents the sponsor in the Standardized Vocabularies.","payer_plan_period"
|
|
||||||
"sponsor_source_value","No","VARCHAR(50)","The source code for the Person's sponsor of the health plan as it appears in the source data.","payer_plan_period"
|
|
||||||
"sponsor_source_concept_id","Yes","INTEGER","A foreign key to a sponsor concept that refers to the sponsor code used in the source data.","payer_plan_period"
|
|
||||||
"family_source_value","No","VARCHAR(50)","The source code for the Person's family as it appears in the source data.","payer_plan_period"
|
|
||||||
"stop_reason_concept_id","Yes","INTEGER","A foreign key that refers to a standard termination reason that represents the reason for the termination in the Standardized Vocabularies.","payer_plan_period"
|
|
||||||
"stop_reason_source_value","No","VARCHAR(50)","The reason for stop-coverage as it appears in the source data.","payer_plan_period"
|
|
||||||
"stop_reason_source_concept_id","Yes","INTEGER","A foreign key to a stop-coverage concept that refers to the code used in the source.","payer_plan_period"
|
|
||||||
"care_site_id","Yes","INTEGER","A unique identifier for each Care Site.","care_site"
|
|
||||||
"care_site_name","No","VARCHAR(255)","The verbatim description or name of the Care Site as in data source","care_site"
|
|
||||||
"place_of_service_concept_id","Yes","INTEGER","A foreign key that refers to a Place of Service Concept ID in the Standardized Vocabularies.","care_site"
|
|
||||||
"location_id","No","INTEGER","A foreign key to the geographic Location in the LOCATION table, where the detailed address information is stored.","care_site"
|
|
||||||
"care_site_source_value","No","VARCHAR(50)","The identifier for the Care Site in the source data, stored here for reference.","care_site"
|
|
||||||
"place_of_service_source_value","No","VARCHAR(50)","The source code for the Place of Service as it appears in the source data, stored here for reference.","care_site"
|
|
||||||
"location_id","Yes","INTEGER","A unique identifier for each geographic location.","location"
|
|
||||||
"address_1","No","VARCHAR(50)","The address field 1, typically used for the street address, as it appears in the source data.","location"
|
|
||||||
"address_2","No","VARCHAR(50)","The address field 2, typically used for additional detail such as buildings, suites, floors, as it appears in the source data.","location"
|
|
||||||
"city","No","VARCHAR(50)","The city field as it appears in the source data.","location"
|
|
||||||
"state","No","VARCHAR(2)","The state field as it appears in the source data.","location"
|
|
||||||
"zip","No","VARCHAR(9)","The zip or postal code.","location"
|
|
||||||
"county","No","VARCHAR(20)","The county.","location"
|
|
||||||
"country","No","VARCHAR(100)","The country","location"
|
|
||||||
"location_source_value","No","VARCHAR(50)","The verbatim information that is used to uniquely identify the location as it appears in the source data.","location"
|
|
||||||
"latitude","No","FLOAT","The geocoded latitude","location"
|
|
||||||
"longitude","No","FLOAT","The geocoded longitude","location"
|
|
||||||
"location_id","Yes","INTEGER","A foreign key to the location table.","location_history"
|
|
||||||
"relationship_type_concept_id","Yes","VARCHAR(50)","The type of relationship between location and entity.","location_history"
|
|
||||||
"domain_id","Yes","VARCHAR(50)","The domain of the entity that is related to the location. Either PERSON, PROVIDER, or CARE_SITE.","location_history"
|
|
||||||
"entity_id","Yes","INTEGER","The unique identifier for the entity. References either person_id, provider_id, or care_site_id, depending on domain_id.","location_history"
|
|
||||||
"start_date","Yes","DATE","The date the relationship started.","location_history"
|
|
||||||
"end_date","No","DATE","The date the relationship ended.","location_history"
|
|
||||||
"provider_id","Yes","INTEGER","A unique identifier for each Provider.","provider"
|
|
||||||
"provider_name","No","VARCHAR(255)","A description of the Provider.","provider"
|
|
||||||
"npi","No","VARCHAR(20)","The National Provider Identifier (NPI) of the provider.","provider"
|
|
||||||
"dea","No","VARCHAR(20)","The Drug Enforcement Administration (DEA) number of the provider.","provider"
|
|
||||||
"specialty_concept_id","Yes","INTEGER","A foreign key to a Standard Specialty Concept ID in the Standardized Vocabularies.","provider"
|
|
||||||
"care_site_id","No","INTEGER","A foreign key to the main Care Site where the provider is practicing.","provider"
|
|
||||||
"year_of_birth","No","INTEGER","The year of birth of the Provider.","provider"
|
|
||||||
"gender_concept_id","Yes","INTEGER","The gender of the Provider.","provider"
|
|
||||||
"provider_source_value","No","VARCHAR(50)","The identifier used for the Provider in the source data, stored here for reference.","provider"
|
|
||||||
"specialty_source_value","No","VARCHAR(50)","The source code for the Provider specialty as it appears in the source data, stored here for reference.","provider"
|
|
||||||
"specialty_source_concept_id","Yes","INTEGER","A foreign key to a Concept that refers to the code used in the source.","provider"
|
|
||||||
"gender_source_value","No","VARCHAR(50)","The gender code for the Provider as it appears in the source data, stored here for reference.","provider"
|
|
||||||
"gender_source_concept_id","Yes","INTEGER","A foreign key to a Concept that refers to the code used in the source.","provider"
|
|
||||||
"cdm_source_name","Yes","VARCHAR(255)","The full name of the source","cdm_source"
|
|
||||||
"cdm_source_abbreviation","No","VARCHAR(25)","An abbreviation of the name","cdm_source"
|
|
||||||
"cdm_holder","No","VARCHAR(255)","The name of the organization responsible for the development of the CDM instance","cdm_source"
|
|
||||||
"source_description","No","CLOB","A description of the source data origin and purpose for collection. The description may contain a summary of the period of time that is expected to be covered by this dataset.","cdm_source"
|
|
||||||
"source_documentation_reference","No","VARCHAR(255)","URL or other external reference to location of source documentation","cdm_source"
|
|
||||||
"cdm_etl_reference","No","VARCHAR(255)","URL or other external reference to location of ETL specification documentation and ETL source code","cdm_source"
|
|
||||||
"source_release_date","No","DATE","The date for which the source data are most current, such as the last day of data capture","cdm_source"
|
|
||||||
"cdm_release_date","No","DATE","The date when the CDM was instantiated","cdm_source"
|
|
||||||
"cdm_version","No","VARCHAR(10)","The version of CDM used","cdm_source"
|
|
||||||
"vocabulary_version","No","VARCHAR(20)","The version of the vocabulary used","cdm_source"
|
|
||||||
"metadata_concept_id","Yes","INTEGER","A foreign key that refers to a Standard Metadata Concept identifier in the Standardized Vocabularies.","metadata"
|
|
||||||
"metadata_type_concept_id","Yes","INTEGER","A foreign key that refers to a Standard Type Concept identifier in the Standardized Vocabularies.","metadata"
|
|
||||||
"name","Yes","VARCHAR(250)","The name of the Concept stored in metadata_concept_id or a description of the data being stored.","metadata"
|
|
||||||
"value_as_string","No","NVARCHAR","The metadata value stored as a string.","metadata"
|
|
||||||
"value_as_concept_id","No","INTEGER","A foreign key to a metadata value stored as a Concept ID.","metadata"
|
|
||||||
"metadata date","No","DATE","The date associated with the metadata","metadata"
|
|
||||||
"metadata_datetime","No","DATETIME","The date and time associated with the metadata","metadata"
|
|
||||||
"concept_id","Yes","INTEGER","A unique identifier for each Concept across all domains.","concept"
|
|
||||||
"concept_name","Yes","VARCHAR(255)","An unambiguous, meaningful and descriptive name for the Concept.","concept"
|
|
||||||
"domain_id","Yes","VARCHAR(20)","A foreign key to the [DOMAIN](https://github.com/OHDSI/CommonDataModel/wiki/DOMAIN) table the Concept belongs to.","concept"
|
|
||||||
"vocabulary_id","Yes","VARCHAR(20)","A foreign key to the [VOCABULARY](https://github.com/OHDSI/CommonDataModel/wiki/VOCABULARY) table indicating from which source the Concept has been adapted.","concept"
|
|
||||||
"concept_class_id","Yes","VARCHAR(20)","The attribute or concept class of the Concept. Examples are 'Clinical Drug', 'Ingredient', 'Clinical Finding' etc.","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 allowables values are 'S' (Standard Concept) and 'C' (Classification Concept), otherwise the content is NULL.","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.","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.","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.","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.","concept"
|
|
||||||
"ancestor_concept_id","Yes","INTEGER","A foreign key to the concept in the concept table for the higher-level concept that forms the ancestor in the relationship.","concept_ancestor"
|
|
||||||
"descendant_concept_id","Yes","INTEGER","A foreign key to the concept in the concept table for the lower-level concept that forms the descendant in the relationship.","concept_ancestor"
|
|
||||||
"min_levels_of_separation","Yes","INTEGER","The minimum separation in number of levels of hierarchy between ancestor and descendant concepts. This is an attribute that is used to simplify hierarchic analysis.","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.","concept_ancestor"
|
|
||||||
"concept_class_id","Yes","VARCHAR(20)","A unique key for each class.","concept_class"
|
|
||||||
"concept_class_name","Yes","VARCHAR(255)","The name describing the Concept Class, e.g. ""Clinical Finding"", ""Ingredient"", etc.","concept_class"
|
|
||||||
"concept_class_concept_id","Yes","INTEGER","A foreign key that refers to an identifier in the [CONCEPT](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT) table for the unique Concept Class the record belongs to.","concept_class"
|
|
||||||
"concept_id_1","Yes","INTEGER","A foreign key to a Concept in the [CONCEPT](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT) table associated with the relationship. Relationships are directional, and this field represents the source concept designation.","concept_relationship"
|
|
||||||
"concept_id_2","Yes","INTEGER","A foreign key to a Concept in the [CONCEPT](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT) table associated with the relationship. Relationships are directional, and this field represents the destination concept designation.","concept_relationship"
|
|
||||||
"relationship_id","Yes","VARCHAR(20)","A unique identifier to the type or nature of the Relationship as defined in the [RELATIONSHIP](https://github.com/OHDSI/CommonDataModel/wiki/RELATIONSHIP) table.","concept_relationship"
|
|
||||||
"valid_start_date","Yes","DATE","The date when the instance of the Concept Relationship is first recorded.","concept_relationship"
|
|
||||||
"valid_end_date","Yes","DATE","The date when the Concept Relationship became invalid because it was deleted or superseded (updated) by a new relationship. Default value is 31-Dec-2099.","concept_relationship"
|
|
||||||
"invalid_reason","No","VARCHAR(1)","Reason the relationship was invalidated. Possible values are 'D' (deleted), 'U' (replaced with an update) or NULL when valid_end_date has the default value.","concept_relationship"
|
|
||||||
"concept_id","Yes","INTEGER","A foreign key to the Concept in the CONCEPT table.","concept_synonym"
|
|
||||||
"concept_synonym_name","Yes","VARCHAR(1000)","The alternative name for the Concept.","concept_synonym"
|
|
||||||
"language_concept_id","Yes","INTEGER","A foreign key to a Concept representing the language.","concept_synonym"
|
|
||||||
"domain_id","Yes","VARCHAR(20)","A unique key for each domain.","domain"
|
|
||||||
"domain_name","Yes","VARCHAR(255)","The name describing the Domain, e.g. ""Condition"", ""Procedure"", ""Measurement"" etc.","domain"
|
|
||||||
"domain_concept_id","Yes","INTEGER","A foreign key that refers to an identifier in the [CONCEPT](https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT) table for the unique Domain Concept the Domain record belongs to.","domain"
|
|
||||||
"drug_concept_id","Yes","INTEGER","A foreign key to the Concept in the CONCEPT table representing the identifier for Branded Drug or Clinical Drug Concept.","drug_strength"
|
|
||||||
"ingredient_concept_id","Yes","INTEGER","A foreign key to the Concept in the CONCEPT table, representing the identifier for drug Ingredient Concept contained within the drug product.","drug_strength"
|
|
||||||
"amount_value","No","FLOAT","The numeric value associated with the amount of active ingredient contained within the product.","drug_strength"
|
|
||||||
"amount_unit_concept_id","No","INTEGER","A foreign key to the Concept in the CONCEPT table representing the identifier for the Unit for the absolute amount of active ingredient.","drug_strength"
|
|
||||||
"numerator_value","No","FLOAT","The numeric value associated with the concentration of the active ingredient contained in the product","drug_strength"
|
|
||||||
"numerator_unit_concept_id","No","INTEGER","A foreign key to the Concept in the CONCEPT table representing the identifier for the numerator Unit for the concentration of active ingredient.","drug_strength"
|
|
||||||
"denominator_value","No","FLOAT","The amount of total liquid (or other divisible product, such as ointment, gel, spray, etc.).","drug_strength"
|
|
||||||
"denominator_unit_concept_id","No","INTEGER","A foreign key to the Concept in the CONCEPT table representing the identifier for the denominator Unit for the concentration of active ingredient.","drug_strength"
|
|
||||||
"box_size","No","INTEGER","The number of units of Clinical of Branded Drug, or Quantified Clinical or Branded Drug contained in a box as dispensed to the patient","drug_strength"
|
|
||||||
"valid_start_date","Yes","DATE","The date when the Concept was first recorded. The default value is 1-Jan-1970.","drug_strength"
|
|
||||||
"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.","drug_strength"
|
|
||||||
"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.","drug_strength"
|
|
||||||
"relationship_id","Yes","VARCHAR(20)","The type of relationship captured by the relationship record.","relationship"
|
|
||||||
"relationship_name","Yes","VARCHAR(255)","The text that describes the relationship type.","relationship"
|
|
||||||
"is_hierarchical","Yes","VARCHAR(1)","Defines whether a relationship defines concepts into classes or hierarchies. Values are 1 for hierarchical relationship or 0 if not.","relationship"
|
|
||||||
"defines_ancestry","Yes","VARCHAR(1)","Defines whether a hierarchical relationship contributes to the concept_ancestor table. These are subsets of the hierarchical relationships. Valid values are 1 or 0.","relationship"
|
|
||||||
"reverse_relationship_id","Yes","VARCHAR(20)","The identifier for the relationship used to define the reverse relationship between two concepts.","relationship"
|
|
||||||
"relationship_concept_id","Yes","INTEGER","A foreign key that refers to an identifier in the CONCEPT table for the unique relationship concept.","relationship"
|
|
||||||
"source_code","Yes","VARCHAR(50)","The source code being translated into a Standard Concept.","source_to_concept_map"
|
|
||||||
"source_concept_id","Yes","INTEGER","A foreign key to the Source Concept that is being translated into a Standard Concept.","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.","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.","source_to_concept_map"
|
|
||||||
"target_concept_id","Yes","INTEGER","A foreign key to the target Concept to which the source code is being mapped.","source_to_concept_map"
|
|
||||||
"target_vocabulary_id","Yes","VARCHAR(20)","A foreign key to the VOCABULARY table defining the vocabulary of the target Concept.","source_to_concept_map"
|
|
||||||
"valid_start_date","Yes","DATE","The date when the mapping instance was first recorded.","source_to_concept_map"
|
|
||||||
"valid_end_date","Yes","DATE","The date when the mapping instance became invalid because it was deleted or superseded (updated) by a new relationship. Default value is 31-Dec-2099.","source_to_concept_map"
|
|
||||||
"invalid_reason","No","VARCHAR(1)","Reason the mapping instance was invalidated. Possible values are D (deleted), U (replaced with an update) or NULL when valid_end_date has the default value.","source_to_concept_map"
|
|
||||||
"vocabulary_id","Yes","VARCHAR(20)","A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit.","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.","vocabulary"
|
|
||||||
"vocabulary_reference","Yes","VARCHAR(255)","External reference to documentation or available download of the about the vocabulary.","vocabulary"
|
|
||||||
"vocabulary_version","No","VARCHAR(255)","Version of the Vocabulary as indicated in the source.","vocabulary"
|
|
||||||
"vocabulary_concept_id","Yes","INTEGER","A foreign key that refers to a standard concept identifier in the CONCEPT table for the Vocabulary the VOCABULARY record belongs to.","vocabulary"
|
|
||||||
|
|
|
@ -0,0 +1,417 @@
|
||||||
|
<!DOCTYPE html>
|
||||||
|
|
||||||
|
<html xmlns="http://www.w3.org/1999/xhtml">
|
||||||
|
|
||||||
|
<head>
|
||||||
|
|
||||||
|
<meta charset="utf-8" />
|
||||||
|
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
||||||
|
<meta name="generator" content="pandoc" />
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
<title>CDM Proposals Under Review</title>
|
||||||
|
|
||||||
|
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
|
||||||
|
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||||
|
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
|
||||||
|
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
|
||||||
|
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
|
||||||
|
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
|
||||||
|
<script src="site_libs/navigation-1.1/tabsets.js"></script>
|
||||||
|
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
|
||||||
|
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
|
||||||
|
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
|
||||||
|
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
|
||||||
|
<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
|
||||||
|
|
||||||
|
<style type="text/css">code{white-space: pre;}</style>
|
||||||
|
<style type="text/css">
|
||||||
|
pre:not([class]) {
|
||||||
|
background-color: white;
|
||||||
|
}
|
||||||
|
</style>
|
||||||
|
<script type="text/javascript">
|
||||||
|
if (window.hljs) {
|
||||||
|
hljs.configure({languages: []});
|
||||||
|
hljs.initHighlightingOnLoad();
|
||||||
|
if (document.readyState && document.readyState === "complete") {
|
||||||
|
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
</script>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
<style type="text/css">
|
||||||
|
h1 {
|
||||||
|
font-size: 34px;
|
||||||
|
}
|
||||||
|
h1.title {
|
||||||
|
font-size: 38px;
|
||||||
|
}
|
||||||
|
h2 {
|
||||||
|
font-size: 30px;
|
||||||
|
}
|
||||||
|
h3 {
|
||||||
|
font-size: 24px;
|
||||||
|
}
|
||||||
|
h4 {
|
||||||
|
font-size: 18px;
|
||||||
|
}
|
||||||
|
h5 {
|
||||||
|
font-size: 16px;
|
||||||
|
}
|
||||||
|
h6 {
|
||||||
|
font-size: 12px;
|
||||||
|
}
|
||||||
|
.table th:not([align]) {
|
||||||
|
text-align: left;
|
||||||
|
}
|
||||||
|
</style>
|
||||||
|
|
||||||
|
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||||
|
|
||||||
|
</head>
|
||||||
|
|
||||||
|
<body>
|
||||||
|
|
||||||
|
<style type = "text/css">
|
||||||
|
.main-container {
|
||||||
|
max-width: 940px;
|
||||||
|
margin-left: auto;
|
||||||
|
margin-right: auto;
|
||||||
|
}
|
||||||
|
code {
|
||||||
|
color: inherit;
|
||||||
|
background-color: rgba(0, 0, 0, 0.04);
|
||||||
|
}
|
||||||
|
img {
|
||||||
|
max-width:100%;
|
||||||
|
height: auto;
|
||||||
|
}
|
||||||
|
.tabbed-pane {
|
||||||
|
padding-top: 12px;
|
||||||
|
}
|
||||||
|
.html-widget {
|
||||||
|
margin-bottom: 20px;
|
||||||
|
}
|
||||||
|
button.code-folding-btn:focus {
|
||||||
|
outline: none;
|
||||||
|
}
|
||||||
|
summary {
|
||||||
|
display: list-item;
|
||||||
|
}
|
||||||
|
</style>
|
||||||
|
|
||||||
|
|
||||||
|
<style type="text/css">
|
||||||
|
/* padding for bootstrap navbar */
|
||||||
|
body {
|
||||||
|
padding-top: 51px;
|
||||||
|
padding-bottom: 40px;
|
||||||
|
}
|
||||||
|
/* offset scroll position for anchor links (for fixed navbar) */
|
||||||
|
.section h1 {
|
||||||
|
padding-top: 56px;
|
||||||
|
margin-top: -56px;
|
||||||
|
}
|
||||||
|
.section h2 {
|
||||||
|
padding-top: 56px;
|
||||||
|
margin-top: -56px;
|
||||||
|
}
|
||||||
|
.section h3 {
|
||||||
|
padding-top: 56px;
|
||||||
|
margin-top: -56px;
|
||||||
|
}
|
||||||
|
.section h4 {
|
||||||
|
padding-top: 56px;
|
||||||
|
margin-top: -56px;
|
||||||
|
}
|
||||||
|
.section h5 {
|
||||||
|
padding-top: 56px;
|
||||||
|
margin-top: -56px;
|
||||||
|
}
|
||||||
|
.section h6 {
|
||||||
|
padding-top: 56px;
|
||||||
|
margin-top: -56px;
|
||||||
|
}
|
||||||
|
.dropdown-submenu {
|
||||||
|
position: relative;
|
||||||
|
}
|
||||||
|
.dropdown-submenu>.dropdown-menu {
|
||||||
|
top: 0;
|
||||||
|
left: 100%;
|
||||||
|
margin-top: -6px;
|
||||||
|
margin-left: -1px;
|
||||||
|
border-radius: 0 6px 6px 6px;
|
||||||
|
}
|
||||||
|
.dropdown-submenu:hover>.dropdown-menu {
|
||||||
|
display: block;
|
||||||
|
}
|
||||||
|
.dropdown-submenu>a:after {
|
||||||
|
display: block;
|
||||||
|
content: " ";
|
||||||
|
float: right;
|
||||||
|
width: 0;
|
||||||
|
height: 0;
|
||||||
|
border-color: transparent;
|
||||||
|
border-style: solid;
|
||||||
|
border-width: 5px 0 5px 5px;
|
||||||
|
border-left-color: #cccccc;
|
||||||
|
margin-top: 5px;
|
||||||
|
margin-right: -10px;
|
||||||
|
}
|
||||||
|
.dropdown-submenu:hover>a:after {
|
||||||
|
border-left-color: #ffffff;
|
||||||
|
}
|
||||||
|
.dropdown-submenu.pull-left {
|
||||||
|
float: none;
|
||||||
|
}
|
||||||
|
.dropdown-submenu.pull-left>.dropdown-menu {
|
||||||
|
left: -100%;
|
||||||
|
margin-left: 10px;
|
||||||
|
border-radius: 6px 0 6px 6px;
|
||||||
|
}
|
||||||
|
</style>
|
||||||
|
|
||||||
|
<script>
|
||||||
|
// manage active state of menu based on current page
|
||||||
|
$(document).ready(function () {
|
||||||
|
// active menu anchor
|
||||||
|
href = window.location.pathname
|
||||||
|
href = href.substr(href.lastIndexOf('/') + 1)
|
||||||
|
if (href === "")
|
||||||
|
href = "index.html";
|
||||||
|
var menuAnchor = $('a[href="' + href + '"]');
|
||||||
|
|
||||||
|
// mark it active
|
||||||
|
menuAnchor.parent().addClass('active');
|
||||||
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|
||||||
|
// if it's got a parent navbar menu mark it active as well
|
||||||
|
menuAnchor.closest('li.dropdown').addClass('active');
|
||||||
|
});
|
||||||
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</script>
|
||||||
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|
||||||
|
<div class="container-fluid main-container">
|
||||||
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||||||
|
<!-- tabsets -->
|
||||||
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|
||||||
|
<style type="text/css">
|
||||||
|
.tabset-dropdown > .nav-tabs {
|
||||||
|
display: inline-table;
|
||||||
|
max-height: 500px;
|
||||||
|
min-height: 44px;
|
||||||
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overflow-y: auto;
|
||||||
|
background: white;
|
||||||
|
border: 1px solid #ddd;
|
||||||
|
border-radius: 4px;
|
||||||
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}
|
||||||
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|
||||||
|
.tabset-dropdown > .nav-tabs > li.active:before {
|
||||||
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content: "";
|
||||||
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font-family: 'Glyphicons Halflings';
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display: inline-block;
|
||||||
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padding: 10px;
|
||||||
|
border-right: 1px solid #ddd;
|
||||||
|
}
|
||||||
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||||||
|
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
|
||||||
|
content: "";
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||||||
|
border: none;
|
||||||
|
}
|
||||||
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|
||||||
|
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||||
|
content: "";
|
||||||
|
font-family: 'Glyphicons Halflings';
|
||||||
|
display: inline-block;
|
||||||
|
padding: 10px;
|
||||||
|
border-right: 1px solid #ddd;
|
||||||
|
}
|
||||||
|
|
||||||
|
.tabset-dropdown > .nav-tabs > li.active {
|
||||||
|
display: block;
|
||||||
|
}
|
||||||
|
|
||||||
|
.tabset-dropdown > .nav-tabs > li > a,
|
||||||
|
.tabset-dropdown > .nav-tabs > li > a:focus,
|
||||||
|
.tabset-dropdown > .nav-tabs > li > a:hover {
|
||||||
|
border: none;
|
||||||
|
display: inline-block;
|
||||||
|
border-radius: 4px;
|
||||||
|
}
|
||||||
|
|
||||||
|
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
|
||||||
|
display: block;
|
||||||
|
float: none;
|
||||||
|
}
|
||||||
|
|
||||||
|
.tabset-dropdown > .nav-tabs > li {
|
||||||
|
display: none;
|
||||||
|
}
|
||||||
|
</style>
|
||||||
|
|
||||||
|
<script>
|
||||||
|
$(document).ready(function () {
|
||||||
|
window.buildTabsets("TOC");
|
||||||
|
});
|
||||||
|
|
||||||
|
$(document).ready(function () {
|
||||||
|
$('.tabset-dropdown > .nav-tabs > li').click(function () {
|
||||||
|
$(this).parent().toggleClass('nav-tabs-open')
|
||||||
|
});
|
||||||
|
});
|
||||||
|
</script>
|
||||||
|
|
||||||
|
<!-- code folding -->
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||||
|
<div class="container">
|
||||||
|
<div class="navbar-header">
|
||||||
|
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
|
||||||
|
<span class="icon-bar"></span>
|
||||||
|
<span class="icon-bar"></span>
|
||||||
|
<span class="icon-bar"></span>
|
||||||
|
</button>
|
||||||
|
<a class="navbar-brand" href="index.html"><div><img src="ohdsi16x16.png"></img> OMOP Common Data Model </div></a>
|
||||||
|
</div>
|
||||||
|
<div id="navbar" class="navbar-collapse collapse">
|
||||||
|
<ul class="nav navbar-nav">
|
||||||
|
<li>
|
||||||
|
<a href="index.html">
|
||||||
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="background.html">
|
||||||
|
<span class="fa fa-landmark"></span>
|
||||||
|
|
||||||
|
Background
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="dataModelConventions.html">
|
||||||
|
<span class="fa fa-list-alt"></span>
|
||||||
|
|
||||||
|
Conventions
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
|
<li class="dropdown">
|
||||||
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
|
<span class="fa fa-history"></span>
|
||||||
|
|
||||||
|
CDM Versions
|
||||||
|
|
||||||
|
<span class="caret"></span>
|
||||||
|
</a>
|
||||||
|
<ul class="dropdown-menu" role="menu">
|
||||||
|
<li>
|
||||||
|
<a href="cdm531.html">CDM v5.3.1</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="cdm60.html">CDM v6.0</a>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</li>
|
||||||
|
<li class="dropdown">
|
||||||
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
|
<span class="fa fa-plus-square"></span>
|
||||||
|
|
||||||
|
Proposals
|
||||||
|
|
||||||
|
<span class="caret"></span>
|
||||||
|
</a>
|
||||||
|
<ul class="dropdown-menu" role="menu">
|
||||||
|
<li>
|
||||||
|
<a href="reviewProposals.html">Under Review</a>
|
||||||
|
</li>
|
||||||
|
<li class="dropdown-submenu">
|
||||||
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||||
|
<ul class="dropdown-menu" role="menu">
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/files/2642492/Oncology.CDM.Proposal.2018-12-02.pdf">Oncology CDM Proposal</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="faq.html">
|
||||||
|
<span class="fa fa-question"></span>
|
||||||
|
|
||||||
|
FAQ
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<a href="contribute.html">
|
||||||
|
<span class="fa fa-wrench"></span>
|
||||||
|
|
||||||
|
Contribute
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
<ul class="nav navbar-nav navbar-right">
|
||||||
|
<li>
|
||||||
|
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||||
|
<span class="fa fa-github fa-lg"></span>
|
||||||
|
|
||||||
|
</a>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</div><!--/.nav-collapse -->
|
||||||
|
</div><!--/.container -->
|
||||||
|
</div><!--/.navbar -->
|
||||||
|
|
||||||
|
<div class="fluid-row" id="header">
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
<h1 class="title toc-ignore">CDM Proposals Under Review</h1>
|
||||||
|
|
||||||
|
</div>
|
||||||
|
|
||||||
|
|
||||||
|
<p>This page is still in development. For a list of all proposals currently under review please see the <a href="https://github.com/OHDSI/CommonDataModel/issues?utf8=%E2%9C%93&q=is%3Aissue%20label%3AProposal%20">github issue log</a>.</p>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<script>
|
||||||
|
|
||||||
|
// add bootstrap table styles to pandoc tables
|
||||||
|
function bootstrapStylePandocTables() {
|
||||||
|
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
|
||||||
|
}
|
||||||
|
$(document).ready(function () {
|
||||||
|
bootstrapStylePandocTables();
|
||||||
|
});
|
||||||
|
|
||||||
|
|
||||||
|
</script>
|
||||||
|
|
||||||
|
<!-- dynamically load mathjax for compatibility with self-contained -->
|
||||||
|
<script>
|
||||||
|
(function () {
|
||||||
|
var script = document.createElement("script");
|
||||||
|
script.type = "text/javascript";
|
||||||
|
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
|
||||||
|
document.getElementsByTagName("head")[0].appendChild(script);
|
||||||
|
})();
|
||||||
|
</script>
|
||||||
|
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
Loading…
Reference in New Issue