1460 lines
35 KiB
HTML
1460 lines
35 KiB
HTML
<!DOCTYPE html>
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<title>OMOP CDM v5.4 Detailed Tooling Support</title>
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</head>
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<body>
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<div class="row">
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<div class="col-xs-12 col-sm-4 col-md-3">
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<div id="TOC" class="tocify">
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</div>
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</div>
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<div class="toc-content col-xs-12 col-sm-8 col-md-9">
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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</button>
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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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</div>
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<div id="navbar" class="navbar-collapse collapse">
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<ul class="nav navbar-nav">
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<a href="index.html">
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<span class="fa fa-house"></span>
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</a>
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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" data-bs-toggle="dropdown" aria-expanded="false">
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<span class="fa fa-landmark"></span>
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Background
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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="background.html">Model Background</a>
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</li>
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<li>
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<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
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</li>
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<li>
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<a href="vocabulary.html">How the Vocabulary is Built</a>
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</li>
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</ul>
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</li>
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<li class="dropdown">
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Conventions
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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="dataModelConventions.html">General Conventions</a>
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</li>
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<li>
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<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
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</li>
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<li>
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<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
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</li>
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</ul>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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<span class="fa fa-history"></span>
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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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<li>
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<a href="cdm30.html">CDM v3.0</a>
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</li>
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<li>
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<a href="cdm53.html">CDM v5.3</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" data-bs-toggle="dropdown" aria-expanded="false">CDM v5.4</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="cdm54.html">CDM v5.4</a>
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</li>
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<li>
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||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
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||
</li>
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||
<li>
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<a href="cdm54erd.html">Entity Relationships</a>
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||
</li>
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<li>
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||
<a href="cdm54ToolingSupport.html">Detailed tooling support per CDM field</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 class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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<span class="fa fa-plus-square"></span>
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CDM 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="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
|
||
</li>
|
||
<li>
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||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">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" data-bs-toggle="dropdown" aria-expanded="false">Accepted</a>
|
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<ul class="dropdown-menu" role="menu">
|
||
<li>
|
||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||
</li>
|
||
</ul>
|
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</li>
|
||
</ul>
|
||
</li>
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<li class="dropdown">
|
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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<span class="fa fa-question"></span>
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How to
|
||
|
||
<span class="caret"></span>
|
||
</a>
|
||
<ul class="dropdown-menu" role="menu">
|
||
<li>
|
||
<a href="download.html">Download the DDL</a>
|
||
</li>
|
||
<li>
|
||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||
</li>
|
||
<li>
|
||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
<li class="dropdown">
|
||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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<span class="fa fa-life-ring"></span>
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|
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Support
|
||
|
||
<span class="caret"></span>
|
||
</a>
|
||
<ul class="dropdown-menu" role="menu">
|
||
<li>
|
||
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
|
||
</li>
|
||
<li>
|
||
<a href="faq.html">FAQ</a>
|
||
</li>
|
||
<li>
|
||
<a href="sqlScripts.html">SQL Scripts</a>
|
||
</li>
|
||
<li>
|
||
<a href="contribute.html">Ask a Question</a>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<ul class="nav navbar-nav navbar-right">
|
||
<li>
|
||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||
<span class="fa fa-github"></span>
|
||
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
</div><!--/.nav-collapse -->
|
||
</div><!--/.container -->
|
||
</div><!--/.navbar -->
|
||
|
||
<div id="header">
|
||
|
||
|
||
|
||
<h1 class="title toc-ignore"><strong>OMOP CDM v5.4 Detailed Tooling
|
||
Support</strong></h1>
|
||
|
||
</div>
|
||
|
||
|
||
<div id="introduction" class="section level1">
|
||
<h1>Introduction</h1>
|
||
<p>This tables below contain an overview of which standard OHDSI tools
|
||
make use of which OMOP CDM fields. The goal is to inform ETL developers,
|
||
tooling developers and CDM extensions.</p>
|
||
<ul>
|
||
<li>For ETL developers it helps to have guidance on which fieds to
|
||
prioritise in the mapping. Most value will be gained from populating
|
||
fields support across the OHDSI tooling.</li>
|
||
<li>For OHDSI tooling developers, this page provides insight in the gaps
|
||
of support and can drive future development efforts.</li>
|
||
<li>For CDM extenstions, it helps to known what it means for an OMOP CDM
|
||
table/field to be part of the standard. In other words: what OHDSI
|
||
tooling do we at least expect to support the new extensions?</li>
|
||
</ul>
|
||
<p>Currently four OHDSI tools have been evaluated: DataQualityDashboard,
|
||
Achilles, Atlas (Data Sources and Cohort creation) and Feature
|
||
Extraction.</p>
|
||
<div id="criteria" class="section level2">
|
||
<h2>Criteria</h2>
|
||
<table>
|
||
<colgroup>
|
||
<col width="33%" />
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||
<col width="33%" />
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||
<col width="33%" />
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||
</colgroup>
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||
<thead>
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||
<tr class="header">
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||
<th>Tool</th>
|
||
<th>Supports CDM Field if</th>
|
||
<th>Link to resource used</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>DataQualityDashboard</td>
|
||
<td>Part of Field Level checks</td>
|
||
<td><a
|
||
href="https://github.com/OHDSI/DataQualityDashboard/blob/main/inst/csv/OMOP_CDMv5.4_Field_Level.csv"
|
||
class="uri">https://github.com/OHDSI/DataQualityDashboard/blob/main/inst/csv/OMOP_CDMv5.4_Field_Level.csv</a></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>Achilles</td>
|
||
<td>Covered by at least one Achilles analysis</td>
|
||
<td><a
|
||
href="https://github.com/OHDSI/Achilles/blob/main/inst/csv/achilles/achilles_analysis_details.csv"
|
||
class="uri">https://github.com/OHDSI/Achilles/blob/main/inst/csv/achilles/achilles_analysis_details.csv</a></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>Atlas Data Sources</td>
|
||
<td>A statistic based on the field is shown in a ‘Data Sources’
|
||
visualisation</td>
|
||
<td><a href="https://atlas-demo.ohdsi.org/"
|
||
class="uri">https://atlas-demo.ohdsi.org/</a></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>Atlas Cohort</td>
|
||
<td>Used in te Atlas User Interface for cohort definition criteria
|
||
(directly, or via ‘Add attribute’)</td>
|
||
<td><a href="https://atlas-demo.ohdsi.org/"
|
||
class="uri">https://atlas-demo.ohdsi.org/</a></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>Feature Extraction</td>
|
||
<td>Used in one of the Feature Extraction analyses</td>
|
||
<td><a
|
||
href="https://github.com/OHDSI/FeatureExtraction/blob/main/inst/csv/"
|
||
class="uri">https://github.com/OHDSI/FeatureExtraction/blob/main/inst/csv/</a></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>General criteria: - ✔️ if the field essential for OMOP CDM definition
|
||
(Primary Key, Foreign Key) e.g. person_id not explicitly used, but
|
||
essential. (if the PK is marked as False, it typically means the whole
|
||
table is not used in the tool e.g. <code>_source_value</code> fields
|
||
that are used for traceability in ETL) - ❗ if field is used by the
|
||
tool, but not in a meaningful way. e.g. <code>provider_id</code> in
|
||
Achilles only checked for a valid foreign key to the provider table.</p>
|
||
</div>
|
||
</div>
|
||
<div id="tooling-support-for-omop-fields" class="section level1">
|
||
<h1>Tooling Support for OMOP fields</h1>
|
||
<table>
|
||
<colgroup>
|
||
<col width="50%" />
|
||
<col width="50%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th><strong>Abbrevations</strong></th>
|
||
<th> </th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td><strong>PK</strong></td>
|
||
<td>Primary Key</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td><strong>SV</strong></td>
|
||
<td>Source Value (for data quality / etl validation)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td><strong>BC</strong></td>
|
||
<td>Backwards Compatibility, to support CDM <v5.4</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td><strong>FC</strong></td>
|
||
<td>Forwards Compatibility, to easy support for CDM v6 in the
|
||
future.</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<div id="person" class="section level2">
|
||
<h2>Person</h2>
|
||
<table>
|
||
<colgroup>
|
||
<col width="6%" />
|
||
<col width="6%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="6%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th>cdmTableName</th>
|
||
<th>cdmFieldName</th>
|
||
<th align="center">Special Fields</th>
|
||
<th align="center">DQD (v1.0)</th>
|
||
<th align="center">Achilles (v1.7)</th>
|
||
<th align="center">Atlas Cohort (v2.10)</th>
|
||
<th align="center">Atlas Cohort (v2.12)</th>
|
||
<th align="center">Atlas Data Sources (v2.12)</th>
|
||
<th align="center">Feature Extraction (v3.2)</th>
|
||
<th>Comment</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>PERSON</td>
|
||
<td>person_id</td>
|
||
<td align="center">PK</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>PERSON</td>
|
||
<td>gender_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>PERSON</td>
|
||
<td>year_of_birth</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>PERSON</td>
|
||
<td>month_of_birth</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>PERSON</td>
|
||
<td>day_of_birth</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>PERSON</td>
|
||
<td>birth_datetime</td>
|
||
<td align="center">FC</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>PERSON</td>
|
||
<td>race_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>PERSON</td>
|
||
<td>ethnicity_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>PERSON</td>
|
||
<td>location_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td>Achilles only does FK check</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>PERSON</td>
|
||
<td>provider_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td>Achilles only does FK check</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>PERSON</td>
|
||
<td>care_site_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td>Achilles only does FK check</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>PERSON</td>
|
||
<td>person_source_value</td>
|
||
<td align="center">SV</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>PERSON</td>
|
||
<td>gender_source_value</td>
|
||
<td align="center">SV</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>PERSON</td>
|
||
<td>gender_source_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>PERSON</td>
|
||
<td>race_source_value</td>
|
||
<td align="center">SV</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>PERSON</td>
|
||
<td>race_source_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>PERSON</td>
|
||
<td>ethnicity_source_value</td>
|
||
<td align="center">SV</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>PERSON</td>
|
||
<td>ethnicity_source_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
<div id="observation-period" class="section level2">
|
||
<h2>Observation Period</h2>
|
||
<table>
|
||
<colgroup>
|
||
<col width="6%" />
|
||
<col width="6%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="6%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th>cdmTableName</th>
|
||
<th>cdmFieldName</th>
|
||
<th align="center">Special Fields</th>
|
||
<th align="center">DQD (v1.0)</th>
|
||
<th align="center">Achilles (v1.7)</th>
|
||
<th align="center">Atlas Cohort (v2.10)</th>
|
||
<th align="center">Atlas Cohort (v2.12)</th>
|
||
<th align="center">Atlas Data Sources (v2.12)</th>
|
||
<th align="center">Feature Extraction (v3.2)</th>
|
||
<th>Comment</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>OBSERVATION_PERIOD</td>
|
||
<td>observation_period_id</td>
|
||
<td align="center">PK</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>OBSERVATION_PERIOD</td>
|
||
<td>person_id</td>
|
||
<td align="center">Pid</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>OBSERVATION_PERIOD</td>
|
||
<td>observation_period_start_date</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>OBSERVATION_PERIOD</td>
|
||
<td>observation_period_end_date</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>OBSERVATION_PERIOD</td>
|
||
<td>period_type_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
<div id="visit-occurrence" class="section level2">
|
||
<h2>Visit Occurrence</h2>
|
||
<table>
|
||
<colgroup>
|
||
<col width="6%" />
|
||
<col width="6%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="6%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th>cdmTableName</th>
|
||
<th>cdmFieldName</th>
|
||
<th align="center">Special Fields</th>
|
||
<th align="center">DQD (v1.0)</th>
|
||
<th align="center">Achilles (v1.7)</th>
|
||
<th align="center">Atlas Cohort (v2.10)</th>
|
||
<th align="center">Atlas Cohort (v2.12)</th>
|
||
<th align="center">Atlas Data Sources (v2.12)</th>
|
||
<th align="center">Feature Extraction (v3.2)</th>
|
||
<th>Comment</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>visit_occurrence_id</td>
|
||
<td align="center">PK</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>person_id</td>
|
||
<td align="center">Pid</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>visit_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>visit_source_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>visit_source_value</td>
|
||
<td align="center">SV</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>visit_start_date</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td>Achilles check 1900</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>visit_start_datetime</td>
|
||
<td align="center">FC</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>visit_end_date</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">✔️</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>visit_end_datetime</td>
|
||
<td align="center">FC</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>visit_type_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>provider_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td>Atlas uses provider.specialty_concept_id</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>care_site_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td>Achilles only does FK check, Atlas uses
|
||
care_site.place_of_service_concept_id</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>admitted_from_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>admitted_from_source_value</td>
|
||
<td align="center">SV</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td>Achilles check 1900</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>discharged_to_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>discharged_to_source_value</td>
|
||
<td align="center">SV</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td>Achilles check 1900</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>VISIT_OCCURRENCE</td>
|
||
<td>preceding_visit_occurrence_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
<div id="episode" class="section level2">
|
||
<h2>Episode</h2>
|
||
<table>
|
||
<colgroup>
|
||
<col width="6%" />
|
||
<col width="6%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="11%" />
|
||
<col width="6%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th>cdmTableName</th>
|
||
<th>cdmFieldName</th>
|
||
<th align="center">Special Fields</th>
|
||
<th align="center">DQD (v1.0)</th>
|
||
<th align="center">Achilles (v1.7)</th>
|
||
<th align="center">Atlas Cohort (v2.10)</th>
|
||
<th align="center">Atlas Cohort (v2.12)</th>
|
||
<th align="center">Atlas Data Sources (v2.12)</th>
|
||
<th align="center">Feature Extraction (v3.2)</th>
|
||
<th>Comment</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>EPISODE</td>
|
||
<td>episode_id</td>
|
||
<td align="center">PK</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>EPISODE</td>
|
||
<td>person_id</td>
|
||
<td align="center">Pid</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>EPISODE</td>
|
||
<td>episode_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>EPISODE</td>
|
||
<td>episode_start_date</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>EPISODE</td>
|
||
<td>episode_start_datetime</td>
|
||
<td align="center">FC</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>EPISODE</td>
|
||
<td>episode_end_date</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>EPISODE</td>
|
||
<td>episode_end_datetime</td>
|
||
<td align="center">FC</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>EPISODE</td>
|
||
<td>episode_parent_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>EPISODE</td>
|
||
<td>episode_number</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>EPISODE</td>
|
||
<td>episode_object_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>EPISODE</td>
|
||
<td>episode_type_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>EPISODE</td>
|
||
<td>episode_source_value</td>
|
||
<td align="center">SV</td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>EPISODE</td>
|
||
<td>episode_source_concept_id</td>
|
||
<td align="center"></td>
|
||
<td align="center">✔️</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td align="center">❗</td>
|
||
<td></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>This was an effort by the CDM Working Group in 2022. *Credits: Clair
|
||
Blacketer, Maxim Moinat, Nitin Park</p>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
</div>
|
||
</div>
|
||
|
||
</div>
|
||
|
||
<script>
|
||
|
||
// add bootstrap table styles to pandoc tables
|
||
function bootstrapStylePandocTables() {
|
||
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
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}
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$(document).ready(function () {
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||
bootstrapStylePandocTables();
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||
});
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||
|
||
|
||
</script>
|
||
|
||
<!-- tabsets -->
|
||
|
||
<script>
|
||
$(document).ready(function () {
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||
window.buildTabsets("TOC");
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});
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$(document).ready(function () {
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$('.tabset-dropdown > .nav-tabs > li').click(function () {
|
||
$(this).parent().toggleClass('nav-tabs-open');
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});
|
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});
|
||
</script>
|
||
|
||
<!-- code folding -->
|
||
|
||
<script>
|
||
$(document).ready(function () {
|
||
|
||
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
|
||
$('.unlisted.unnumbered').addClass('toc-ignore')
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|
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// move toc-ignore selectors from section div to header
|
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$('div.section.toc-ignore')
|
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.removeClass('toc-ignore')
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.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
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// establish options
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var options = {
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theme: "bootstrap3",
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hashGenerator: function (text) {
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return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
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scrollTo: 0
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