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<!DOCTYPE html> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Utility to Load Synthea CSV data to OMOP CDM • ETLSyntheaBuilder</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- 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template-title-body"> <header><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" aria-expanded="false"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">ETLSyntheaBuilder</a> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> <a href="reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> Articles <span class="caret"></span> </a> <ul class="dropdown-menu" role="menu"><li> <a href="articles/Condition_occurrence.html">Condition_occurrence</a> </li> <li> <a href="articles/Drug_exposure.html">Drug_exposure</a> </li> <li> <a href="articles/Measurement.html">Measurement</a> </li> <li> <a href="articles/observation.html">Observation</a> </li> <li> <a href="articles/observation_period.html">Observation_period</a> </li> <li> <a href="articles/person.html">Person</a> </li> <li> <a href="articles/procedure_occurrence.html">Procedure_occurrence</a> </li> <li> <a href="articles/visit_occurrence.html">Visit Occurrence</a> </li> </ul></li> </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> </header><div class="row"> <div class="contents col-md-9"> <div class="page-header"> <h1>Utility to Load Synthea CSV data to OMOP CDM</h1> </div> <div id="utility-to-load-synthea-csv-data-to-omop-cdm" class="section level1"> <div class="section level2"> <h2 id="currently-supports-cdm-v53-and-v54">Currently supports CDM v5.3 and v5.4<a class="anchor" aria-label="anchor" href="#currently-supports-cdm-v53-and-v54"></a></h2> <p>Follow the steps on the <a href="https://github.com/synthetichealth/synthea/wiki" class="external-link">synthea wiki</a> to run the program and generate the files. This builder works off of the csv files, not the fhir files. To do this the <code>exporter.csv.export</code> option in the <code>./src/main/resources/synthea.properties</code> file needs to be set to TRUE.</p> <div class="section level3"> <h3 id="step-by-step-example">Step by Step Example<a class="anchor" aria-label="anchor" href="#step-by-step-example"></a></h3> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> <code class="sourceCode R"> <span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"OHDSI/ETL-Synthea"</span><span class="op">)</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">ETLSyntheaBuilder</span><span class="op">)</span> <span class="co"># We are loading a version 5.4 CDM into a local PostgreSQL database called "synthea10".</span> <span class="co"># The ETLSyntheaBuilder package leverages the OHDSI/CommonDataModel package for CDM creation.</span> <span class="co"># Valid CDM versions are determined by executing CommonDataModel::listSupportedVersions().</span> <span class="co"># The strings representing supported CDM versions are currently "5.3" and "5.4". </span> <span class="co"># The Synthea version we use in this example is 2.7.0. Since Synthea's MASTER branch is always active, we currently</span> <span class="co"># only support version 2.7.0.</span> <span class="co"># The schema to load the Synthea tables is called "native".</span> <span class="co"># The schema to load the Vocabulary and CDM tables is "cdm_synthea10". </span> <span class="co"># The username and pw are "postgres" and "lollipop".</span> <span class="co"># The Synthea and Vocabulary CSV files are located in /tmp/synthea/output/csv and /tmp/Vocabulary_20181119, respectively.</span> <span class="co"># For those interested in seeing the CDM changes from 5.3 to 5.4, please see: http://ohdsi.github.io/CommonDataModel/cdm54Changes.html</span> <span class="va">cd</span> <span class="op"><-</span> <span class="fu">DatabaseConnector</span><span class="fu">::</span><span class="fu"><a href="https://ohdsi.github.io/DatabaseConnector/reference/createConnectionDetails.html" class="external-link">createConnectionDetails</a></span><span class="op">(</span> dbms <span class="op">=</span> <span class="st">"postgresql"</span>, server <span class="op">=</span> <span class="st">"localhost/synthea10"</span>, user <span class="op">=</span> <span class="st">"postgres"</span>, password <span class="op">=</span> <span class="st">"lollipop"</span>, port <span class="op">=</span> <span class="fl">5432</span>, pathToDriver <span class="op">=</span> <span class="st">"d:/drivers"</span> <span class="op">)</span> <span class="va">cdmSchema</span> <span class="op"><-</span> <span class="st">"cdm_synthea10"</span> <span class="va">cdmVersion</span> <span class="op"><-</span> <span class="st">"5.4"</span> <span class="va">syntheaVersion</span> <span class="op"><-</span> <span class="st">"2.7.0"</span> <span class="va">syntheaSchema</span> <span class="op"><-</span> <span class="st">"native"</span> <span class="va">syntheaFileLoc</span> <span class="op"><-</span> <span class="st">"/tmp/synthea/output/csv"</span> <span class="va">vocabFileLoc</span> <span class="op"><-</span> <span class="st">"/tmp/Vocabulary_20181119"</span> <span class="fu">ETLSyntheaBuilder</span><span class="fu">::</span><span class="fu"><a href="reference/CreateCDMTables.html">CreateCDMTables</a></span><span class="op">(</span>connectionDetails <span class="op">=</span> <span class="va">cd</span>, cdmSchema <span class="op">=</span> <span class="va">cdmSchema</span>, cdmVersion <span class="op">=</span> <span class="va">cdmVersion</span><span class="op">)</span> <span class="fu">ETLSyntheaBuilder</span><span class="fu">::</span><span class="fu"><a href="reference/CreateSyntheaTables.html">CreateSyntheaTables</a></span><span class="op">(</span>connectionDetails <span class="op">=</span> <span class="va">cd</span>, syntheaSchema <span class="op">=</span> <span class="va">syntheaSchema</span>, syntheaVersion <span class="op">=</span> <span class="va">syntheaVersion</span><span class="op">)</span> <span class="fu">ETLSyntheaBuilder</span><span class="fu">::</span><span class="fu"><a href="reference/LoadSyntheaTables.html">LoadSyntheaTables</a></span><span class="op">(</span>connectionDetails <span class="op">=</span> <span class="va">cd</span>, syntheaSchema <span class="op">=</span> <span class="va">syntheaSchema</span>, syntheaFileLoc <span class="op">=</span> <span class="va">syntheaFileLoc</span><span class="op">)</span> <span class="fu">ETLSyntheaBuilder</span><span class="fu">::</span><span class="fu"><a href="reference/LoadVocabFromCsv.html">LoadVocabFromCsv</a></span><span class="op">(</span>connectionDetails <span class="op">=</span> <span class="va">cd</span>, cdmSchema <span class="op">=</span> <span class="va">cdmSchema</span>, vocabFileLoc <span class="op">=</span> <span class="va">vocabFileLoc</span><span class="op">)</span> <span class="fu">ETLSyntheaBuilder</span><span class="fu">::</span><span class="fu"><a href="reference/LoadEventTables.html">LoadEventTables</a></span><span class="op">(</span>connectionDetails <span class="op">=</span> <span class="va">cd</span>, cdmSchema <span class="op">=</span> <span class="va">cdmSchema</span>, syntheaSchema <span class="op">=</span> <span class="va">syntheaSchema</span>, cdmVersion <span class="op">=</span> <span class="va">cdmVersion</span>, syntheaVersion <span class="op">=</span> <span class="va">syntheaVersion</span><span class="op">)</span></code></pre></div> </div> <div class="section level3"> <h3 id="simulating-data-with-synthea">Simulating Data with Synthea<a class="anchor" aria-label="anchor" href="#simulating-data-with-synthea"></a></h3> <p>For commented code used to convert the Synthea data see extras/codeToRun.R</p> <p>For more information on Synthea visit: <a href="https://synthetichealth.github.io/synthea/" class="external-link uri">https://synthetichealth.github.io/synthea/</a></p> <p>Get Synthea from GitHub: <a href="https://github.com/synthetichealth/synthea" class="external-link uri">https://github.com/synthetichealth/synthea</a></p> </div> </div> </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> </nav></div> </div> <footer><div class="copyright"> <p></p><p>Developed by Anthony Molinaro.</p> </div> <div class="pkgdown"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p> </div> </footer></div> </body></html>