1415 lines
40 KiB
HTML
1415 lines
40 KiB
HTML
<!DOCTYPE html>
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<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
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<title>How the Vocabulary is Built</title>
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<style>h1 {font-size: 34px;}
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h1.title {font-size: 38px;}
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h3 {font-size: 24px;}
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pre:not([class]) { background-color: white }</style>
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<style type = "text/css">
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.main-container {
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display: inline-table;
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max-height: 500px;
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min-height: 44px;
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border: 1px solid #ddd;
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<style type="text/css">
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#TOC {
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margin: 25px 0px 20px 0px;
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}
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@media (max-width: 768px) {
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#TOC {
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position: relative;
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width: 100%;
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}
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@media print {
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float: right;
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}
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.toc-content {
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padding-left: 30px;
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padding-right: 40px;
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}
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div.main-container {
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max-width: 1200px;
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}
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div.tocify {
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width: 20%;
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max-width: 260px;
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max-height: 85%;
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}
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@media (min-width: 768px) and (max-width: 991px) {
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div.tocify {
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width: 25%;
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.tocify ul, .tocify li {
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border-radius: 0px;
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</head>
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<body>
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<div class="container-fluid main-container">
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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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</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>
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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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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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<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
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</li>
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<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
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CDM Versions
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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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<a href="cdm53.html">CDM v5.3</a>
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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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<a href="cdm54.html">CDM v5.4</a>
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<a href="cdm54Changes.html">Changes from CDM v5.3</a>
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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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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>
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</li>
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<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 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">
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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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</ul>
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</li>
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</ul>
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How to
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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="download.html">Download the DDL</a>
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</li>
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<li>
|
||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||
</li>
|
||
<li>
|
||
<a href="drug_dose.html">Calculate Drug Dose</a>
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</li>
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</ul>
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Support
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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="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
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<a href="faq.html">FAQ</a>
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<a href="sqlScripts.html">SQL Scripts</a>
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</li>
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<a href="contribute.html">Ask a Question</a>
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<ul class="nav navbar-nav navbar-right">
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<a href="https://github.com/OHDSI/CommonDataModel">
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</a>
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</ul>
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</div><!--/.nav-collapse -->
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</div><!--/.container -->
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</div><!--/.navbar -->
|
||
|
||
<div id="header">
|
||
|
||
|
||
|
||
<h1 class="title toc-ignore">How the Vocabulary is Built</h1>
|
||
|
||
</div>
|
||
|
||
|
||
<div id="mapping-of-concepts" class="section level1">
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||
<h1>Mapping of Concepts</h1>
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||
<p><strong>Mapping</strong>, also known as <strong>a map</strong>, is an
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||
association between a particular concept in one code system or dataset
|
||
and code in another, rarely the same, code system that has the same (or
|
||
similar) meaning. Also, <strong>Mapping</strong> is the process to
|
||
transform one concept into a Standard one. The Standardized Clinical
|
||
Data Tables allow only Standard Concepts, thus all other codes used in
|
||
the source databases have to be translated to Standard Concepts. Mapping
|
||
is done through records in the CONCEPT_RELATIONSHIP table. They connect
|
||
each Concept to a Standard Concept through a number of special
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||
RELATIONSHIP_IDs:</p>
|
||
<table>
|
||
<colgroup>
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<col width="16%" />
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<col width="38%" />
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<col width="44%" />
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</colgroup>
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||
<thead>
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||
<tr class="header">
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||
<th>Relationship ID</th>
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||
<th>Purpose</th>
|
||
<th>Features</th>
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||
</tr>
|
||
</thead>
|
||
<tbody>
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||
<tr class="odd">
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||
<td><strong>Maps to</strong></td>
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||
<td>Mapping a Source Concept to a Standard Concept to be placed into the
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||
following fields of Standardized Clinical Data Tables <br>
|
||
<strong>condition_concept_id</strong><br>
|
||
<strong>observation_concept_id</strong><br><strong>measurement_concept_id</strong><br><strong>drug_concept_id</strong><br><strong>procedure_concept_id</strong><br><strong>device_concept_id</strong>
|
||
Note, that this relationship is also used for mapping of concepts to
|
||
populate <strong>value_as_concept_id</strong></td>
|
||
<td>- Stands for either a full equivalence or an “uphill” mapping
|
||
(mapping to a more general semantic category)<br><br>- Can be single or
|
||
multiple for each Source Concept</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td><strong>Maps to value</strong></td>
|
||
<td>A special mapping between a Source Concept and a Standard Concept to
|
||
be placed into the <strong>value_as_concept_id</strong> field of the
|
||
MEASUREMENT and OBSERVATION tables</td>
|
||
<td>- Points to a concept, indicating the value of Measurements or
|
||
content of Observations<br><br> - Is used only in combination with a
|
||
single “Maps to”</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<div id="maps-to-relationships" class="section level2">
|
||
<h2>“Maps to” Relationships</h2>
|
||
<ul>
|
||
<li>Concepts participating in the “Maps to” mapping are Source
|
||
(Non-standard) Concepts and Standard Concepts.</li>
|
||
<li>The mapping always attempts to reflect the semantics of a Source
|
||
Concept by an Equivalent Standard Concept.</li>
|
||
<li>Equivalent carries the same meaning, covers the same semantic space,
|
||
and, importantly, has the same parents and children in the hierarchy (if
|
||
there are any) as well. If an equivalent Concept is not available, the
|
||
mapping matches to a more generic Standard Concept(s). This ensures that
|
||
a query in the target vocabulary will retrieve the same records as if
|
||
they were queried in the original source vocabulary.</li>
|
||
<li>Source Concepts are mapped or may be mapped to one or several
|
||
Standard Concepts. If they are mapped to more than one Standard Concept,
|
||
in the resulting CDM table, there is more than one record for each
|
||
record in the source.</li>
|
||
<li>Standard Concepts are also mapped to Standard Concepts via “Maps
|
||
to”, this is a mapping to itself.</li>
|
||
<li>If there are 2 or more similar Standard concepts in the OMOP
|
||
vocabulary, please, report about it at the <a
|
||
href="https://forums.ohdsi.org/c/vocabulary-users">OHDSI Forum</a> and
|
||
unless it is fixed, as the first-line choice, use LOINC for Measurements
|
||
and SNOMED for everything else.</li>
|
||
<li>If there are 2 similar Standard concepts within SNOMED, look at the
|
||
domain (Morphologic abnormality is an Observation, Clinical finding is a
|
||
Condition), revise attributes and hierarchy of both concepts (its
|
||
number, fullness, and correctness). It is not necessary to compare the
|
||
amount of relationships/children precisely, just verify that all seems
|
||
appropriate and the hierarchy is rich enough. If it does for both
|
||
concepts, then choose concepts belonging to SNOMED International (short
|
||
concept codes) rather than SNOMED US/UK Editions (long concept codes).
|
||
If the length of concept codes is identical, then choose the one with a
|
||
smaller number of concept_id.</li>
|
||
</ul>
|
||
<p><strong>Note!</strong> Classification Concepts (standard_concept=‘C’)
|
||
do not have a mapping to a Standard Concept.</p>
|
||
<div id="examples-of-usage" class="section level3">
|
||
<h3>Examples of usage:</h3>
|
||
<p><strong>Single “Maps to” for mapping to an Equivalent Standard
|
||
Concept</strong></p>
|
||
<table>
|
||
<colgroup>
|
||
<col width="13%" />
|
||
<col width="18%" />
|
||
<col width="18%" />
|
||
<col width="18%" />
|
||
<col width="13%" />
|
||
<col width="18%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th>Source Concept Code</th>
|
||
<th>Source Concept Name</th>
|
||
<th>Relationship ID</th>
|
||
<th>Standard Concept ID</th>
|
||
<th>Standard Concept Code</th>
|
||
<th>Standard Concept Name</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>M65.3</td>
|
||
<td>Trigger finger</td>
|
||
<td>Maps to</td>
|
||
<td>763891</td>
|
||
<td>448251000124102</td>
|
||
<td>Trigger finger</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>A06</td>
|
||
<td>Amebiasis</td>
|
||
<td>Maps to</td>
|
||
<td>438959</td>
|
||
<td>111910009</td>
|
||
<td>Amebic infection</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p><strong>Single “Maps to” for mapping to a Non-equivalent Standard
|
||
Concept</strong></p>
|
||
<table>
|
||
<colgroup>
|
||
<col width="13%" />
|
||
<col width="18%" />
|
||
<col width="18%" />
|
||
<col width="18%" />
|
||
<col width="13%" />
|
||
<col width="18%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th>Source Concept Code</th>
|
||
<th>Source Concept Name</th>
|
||
<th>Relationship ID</th>
|
||
<th>Standard Concept ID</th>
|
||
<th>Standard Concept Code</th>
|
||
<th>Standard Concept Name</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>D46.5</td>
|
||
<td>Refractory anaemia with multi-lineage dysplasia</td>
|
||
<td>Maps to</td>
|
||
<td>4003185</td>
|
||
<td>109996008</td>
|
||
<td>Refractory anemia</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>M81.50</td>
|
||
<td>Idiopathic osteoporosis, multiple sites</td>
|
||
<td>Maps to</td>
|
||
<td>81390</td>
|
||
<td>3345002</td>
|
||
<td>Idiopathic osteoporosis</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p><strong>Multiple “Maps to” for mapping to several Standard Concepts
|
||
fully covering semantic space of a Source Concept</strong></p>
|
||
<table>
|
||
<colgroup>
|
||
<col width="13%" />
|
||
<col width="18%" />
|
||
<col width="18%" />
|
||
<col width="18%" />
|
||
<col width="13%" />
|
||
<col width="18%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th>Source Concept Code</th>
|
||
<th>Source Concept Name</th>
|
||
<th>Relationship ID</th>
|
||
<th>Standard Concept ID</th>
|
||
<th>Standard Concept Code</th>
|
||
<th>Standard Concept Name</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>S61.1</td>
|
||
<td>Open wound of finger(s) with damage to nail</td>
|
||
<td>Maps to</td>
|
||
<td>4054063</td>
|
||
<td>125653000</td>
|
||
<td>Open wound of finger</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to</td>
|
||
<td>4167909</td>
|
||
<td>275320004</td>
|
||
<td>Injury of nail</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>I26.0</td>
|
||
<td>Pulmonary embolism with mention of acute cor pulmonale</td>
|
||
<td>Maps to</td>
|
||
<td>440417</td>
|
||
<td>59282003</td>
|
||
<td>Pulmonary embolism</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to</td>
|
||
<td>312927</td>
|
||
<td>49584005</td>
|
||
<td>Acute cor pulmonale</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>G44.311</td>
|
||
<td>Acute post-traumatic headache, intractable</td>
|
||
<td>Maps to</td>
|
||
<td>42535403</td>
|
||
<td>290431000119101</td>
|
||
<td>Intractable headache following trauma</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to</td>
|
||
<td>44782681</td>
|
||
<td>122751000119105</td>
|
||
<td>Acute posttraumatic headache</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p><strong>Multiple “Maps to” for mapping to several Standard Concepts
|
||
partially covering semantic space of a Source Concept</strong></p>
|
||
<table>
|
||
<colgroup>
|
||
<col width="13%" />
|
||
<col width="18%" />
|
||
<col width="18%" />
|
||
<col width="18%" />
|
||
<col width="13%" />
|
||
<col width="18%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th>Source Concept Code</th>
|
||
<th>Source Concept Name</th>
|
||
<th>Relationship ID</th>
|
||
<th>Standard Concept ID</th>
|
||
<th>Standard Concept Code</th>
|
||
<th>Standard Concept Name</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>V01.11</td>
|
||
<td>Pedestrian on roller-skates injured in collision with pedal cycle in
|
||
traffic accident</td>
|
||
<td>Maps to</td>
|
||
<td>442247</td>
|
||
<td>215142005</td>
|
||
<td>Pedal cycle accident involving collision between pedal cycle and
|
||
pedestrian, pedestrian injured</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to</td>
|
||
<td>441188</td>
|
||
<td>32906002</td>
|
||
<td>Victim, pedestrian in vehicular AND/OR traffic accident</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>T36.1x4</td>
|
||
<td>Poisoning by cephalosporins and other beta-lactam antibiotics,
|
||
undetermined</td>
|
||
<td>Maps to</td>
|
||
<td>4303975</td>
|
||
<td>419347003</td>
|
||
<td>Poisoning by antibacterial drug</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to</td>
|
||
<td>4055774</td>
|
||
<td>242975003</td>
|
||
<td>Poisoning of undetermined intent by drug</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div id="maps-to-value-relationships" class="section level2">
|
||
<h2>“Maps to value” Relationships</h2>
|
||
<p>To preserve the meaning of Source concepts indicating values of
|
||
Measurements or content of Observations, “Maps to” are complemented with
|
||
a comprehensive set of “Maps to value” relationships. Such mappings are
|
||
considered to be equivalent. There are the following semantic groups of
|
||
Source concepts which are mapped in such a way:</p>
|
||
<ul>
|
||
<li>Conditions indicating abnormal levels of tests</li>
|
||
<li>Encounter for a procedure and an aftercare</li>
|
||
<li>Conditions resulting from the use of devices</li>
|
||
<li>Need for an immunization</li>
|
||
<li>Personal history of a condition</li>
|
||
<li>Family history of a condition</li>
|
||
<li>Personal history of medical treatment or procedure</li>
|
||
<li>Status of a transplant/prosthesis presence</li>
|
||
<li>Patient encounter procedures, not carried out</li>
|
||
</ul>
|
||
<p><strong>Examples of usage:</strong></p>
|
||
<table>
|
||
<colgroup>
|
||
<col width="12%" />
|
||
<col width="15%" />
|
||
<col width="15%" />
|
||
<col width="15%" />
|
||
<col width="12%" />
|
||
<col width="15%" />
|
||
<col width="12%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th>Case #</th>
|
||
<th>Source Concept Code</th>
|
||
<th>Source Concept Name</th>
|
||
<th>Relationship ID</th>
|
||
<th>Standard Concept Code</th>
|
||
<th>Standard Concept Name</th>
|
||
<th>Standard Concept Domain ID</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>1</td>
|
||
<td>R77.0</td>
|
||
<td>Abnormality of albumin</td>
|
||
<td>Maps to</td>
|
||
<td>26758005</td>
|
||
<td>Albumin measurement</td>
|
||
<td>Measurement</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to value</td>
|
||
<td>263654008</td>
|
||
<td>Abnormal</td>
|
||
<td>Spec Disease Status</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>2</td>
|
||
<td>Z47.0</td>
|
||
<td>Follow-up care involving removal of fracture plate and other
|
||
internal fixation device</td>
|
||
<td>Maps to</td>
|
||
<td>390906007</td>
|
||
<td>Follow-up encounter</td>
|
||
<td>Observation</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to value</td>
|
||
<td>72010008</td>
|
||
<td>Removal of internal fixation device</td>
|
||
<td>Procedure</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>3</td>
|
||
<td>Y71</td>
|
||
<td>Cardiovascular devices associated with adverse incidents</td>
|
||
<td>Maps to</td>
|
||
<td>269691005</td>
|
||
<td>Medical accidents to patients during surgical and medical care</td>
|
||
<td>Observation</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to value</td>
|
||
<td>303476002</td>
|
||
<td>Cardiovascular equipment</td>
|
||
<td>Device</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>4</td>
|
||
<td>Z23.2</td>
|
||
<td>Need for immunization against tuberculosis [BCG]</td>
|
||
<td>Maps to</td>
|
||
<td>723620004</td>
|
||
<td>Requires vaccination</td>
|
||
<td>Observation</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to value</td>
|
||
<td>42284007</td>
|
||
<td>BCG vaccination</td>
|
||
<td>Procedure</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>5</td>
|
||
<td>Z86.4</td>
|
||
<td>Personal history of psychoactive substance abuse</td>
|
||
<td>Maps to</td>
|
||
<td>417662000</td>
|
||
<td>History of clinical finding in subject</td>
|
||
<td>Observation</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to value</td>
|
||
<td>91388009</td>
|
||
<td>Psychoactive substance abuse</td>
|
||
<td>Condition</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>6</td>
|
||
<td>Z84.1</td>
|
||
<td>Family history of disorders of kidney and ureter</td>
|
||
<td>Maps to</td>
|
||
<td>416471007</td>
|
||
<td>Family history of clinical finding</td>
|
||
<td>Observation</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to value</td>
|
||
<td>443820000</td>
|
||
<td>Disorder of kidney and/or ureter</td>
|
||
<td>Condition</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>7</td>
|
||
<td>Z92.2</td>
|
||
<td>Personal history of long-term (current) use of other
|
||
medicaments</td>
|
||
<td>Maps to</td>
|
||
<td>416940007</td>
|
||
<td>Past history of procedure</td>
|
||
<td>Observation</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to value</td>
|
||
<td>266713003</td>
|
||
<td>Long-term drug therapy</td>
|
||
<td>Procedure</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>8</td>
|
||
<td>Z96.3</td>
|
||
<td>Presence of artificial larynx</td>
|
||
<td>Maps to</td>
|
||
<td>416940007</td>
|
||
<td>Past history of procedure</td>
|
||
<td>Observation</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to value</td>
|
||
<td>27926003</td>
|
||
<td>Construction of artificial larynx</td>
|
||
<td>Procedure</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>9</td>
|
||
<td>Z53.2</td>
|
||
<td>Procedure not carried out because of patient’s decision for other
|
||
and unspecified reasons</td>
|
||
<td>Maps to</td>
|
||
<td>416237000</td>
|
||
<td>Procedure not done</td>
|
||
<td>Observation</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to value</td>
|
||
<td>105480006</td>
|
||
<td>Refusal of treatment by patient</td>
|
||
<td>Observation</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
<div id="losses-in-mapping" class="section level2">
|
||
<h2>“Losses” in Mapping</h2>
|
||
<p><strong>1. The hierarchical discrepancy between Source and Standard
|
||
Vocabularies</strong></p>
|
||
<p>It is not uncommon for heavily pre-coordinated Concepts (complex and
|
||
fine-grained Concepts that are combinations of different dimensions).
|
||
The coordination depends on the structure of the topology of the
|
||
vocabularies from and to which the Concept is mapped. If they are not
|
||
equivalent, no direct mapping can be established. But in order to
|
||
maintain the ability to retrieve these Concepts when searching using
|
||
hierarchical Concepts, two or more mappings are provided instead.</p>
|
||
<p>For example, in ICD-10-CM diabetic complications are a part of the
|
||
disorder of Diabetes Mellitus, while in SNOMED Diabetes Mellitus and its
|
||
complications reside in distinct hierarchical branches.</p>
|
||
<p><img src="images/diabetes-related_case.png" /></p>
|
||
<p>As another example, ICD-10 codes indicating complications of
|
||
pregnancy are in the chapter of “Pregnancy, childbirth and the
|
||
puerperium” that has a semantic relation to the fact of pregnancy, while
|
||
in SNOMED denoting pregnancy conditions and their complications are in
|
||
the separate hierarchical branches.</p>
|
||
<p><img src="images/pregnancy-related_case.png" /></p>
|
||
<p>The solution for both examples is to map Non-standard concepts to
|
||
several standard ones. Even though there is no distinct equivalent in
|
||
SNOMED, hierarchical queries will retrieve the correct records.</p>
|
||
<p><strong>2. Missing Source Concept equivalent</strong></p>
|
||
<p>This is possible due to the following reasons:</p>
|
||
<p><strong>Vague formulation of a Source Concept</strong></p>
|
||
<table style="width:100%;">
|
||
<colgroup>
|
||
<col width="12%" />
|
||
<col width="16%" />
|
||
<col width="16%" />
|
||
<col width="19%" />
|
||
<col width="19%" />
|
||
<col width="16%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th>source concept code</th>
|
||
<th>source concept name</th>
|
||
<th>relationship ID</th>
|
||
<th>standard concept ID</th>
|
||
<th>standard concept code</th>
|
||
<th>standard concept name</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>M99.9</td>
|
||
<td>Biomechanical lesion, unspecified</td>
|
||
<td>Maps to</td>
|
||
<td>4244662</td>
|
||
<td>928000</td>
|
||
<td>Disorder of musculoskeletal system</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>A28.9</td>
|
||
<td>Zoonotic bacterial disease, unspecified</td>
|
||
<td>Maps to</td>
|
||
<td>432545</td>
|
||
<td>87628006</td>
|
||
<td>Bacterial infectious disease</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p><strong>Source Concept excessive granularity</strong></p>
|
||
<table style="width:100%;">
|
||
<colgroup>
|
||
<col width="12%" />
|
||
<col width="16%" />
|
||
<col width="16%" />
|
||
<col width="19%" />
|
||
<col width="19%" />
|
||
<col width="16%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th>source concept code</th>
|
||
<th>source concept name</th>
|
||
<th>relationship ID</th>
|
||
<th>standard concept ID</th>
|
||
<th>standard concept code</th>
|
||
<th>standard concept name</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>B33.4</td>
|
||
<td>Hantavirus (cardio-)pulmonary syndrome [HPS] [HCPS]</td>
|
||
<td>Maps to</td>
|
||
<td>441784</td>
|
||
<td>359761005</td>
|
||
<td>Disease due to Hantavirus</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>I12.9</td>
|
||
<td>Hypertensive renal disease without renal failure</td>
|
||
<td>Maps to</td>
|
||
<td>201313</td>
|
||
<td>38481006</td>
|
||
<td>Hypertensive renal disease</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>S06.4x9</td>
|
||
<td>Epidural hemorrhage with loss of consciousness of unspecified
|
||
duration</td>
|
||
<td>Maps to</td>
|
||
<td>4306943</td>
|
||
<td>82999001</td>
|
||
<td>Epidural hemorrhage</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to</td>
|
||
<td>372448</td>
|
||
<td>419045004</td>
|
||
<td>Loss of consciousness</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>S35.415</td>
|
||
<td>Laceration of left renal vein</td>
|
||
<td>Maps to</td>
|
||
<td>4124868</td>
|
||
<td>234084003</td>
|
||
<td>Venous laceration</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td></td>
|
||
<td></td>
|
||
<td>Maps to</td>
|
||
<td>195125</td>
|
||
<td>5753006</td>
|
||
<td>Injury of renal vein</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p><strong>Classification difference between Source and Standard
|
||
Vocabularies</strong></p>
|
||
<table style="width:100%;">
|
||
<colgroup>
|
||
<col width="12%" />
|
||
<col width="16%" />
|
||
<col width="16%" />
|
||
<col width="19%" />
|
||
<col width="19%" />
|
||
<col width="16%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th>source concept code</th>
|
||
<th>source concept name</th>
|
||
<th>relationship ID</th>
|
||
<th>standard concept ID</th>
|
||
<th>standard concept code</th>
|
||
<th>standard concept name</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td>I48</td>
|
||
<td>Atrial fibrillation and flutter</td>
|
||
<td>Maps to</td>
|
||
<td>4068155</td>
|
||
<td>17366009</td>
|
||
<td>Atrial arrhythmia</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>G06.0</td>
|
||
<td>Intracranial abscess and granuloma</td>
|
||
<td>Maps to</td>
|
||
<td>4181187</td>
|
||
<td>363176004</td>
|
||
<td>Inflammatory disorder of head</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td>J38.0</td>
|
||
<td>Paralysis of vocal cords and larynx</td>
|
||
<td>Maps to</td>
|
||
<td>4233244</td>
|
||
<td>89927005</td>
|
||
<td>Paralysis of larynx</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td>U82.1</td>
|
||
<td>Resistance to methicillin</td>
|
||
<td>Maps to</td>
|
||
<td>37017452</td>
|
||
<td>713728002</td>
|
||
<td>Drug resistance to antibacterial agent</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p><strong>Other possible issues that one could encounter:</strong></p>
|
||
<ul>
|
||
<li>Mapping has to exist and it can be built, but it is missing. Please
|
||
report to <a href="https://forums.ohdsi.org/">the OHDSI Forum</a>, so it
|
||
can be added.</li>
|
||
<li>Code irrelevant to the patient, for example, ICD-9-CM V65 “Other
|
||
persons seeking consultation”</li>
|
||
<li>Source code is ill-defined, for example, ICD-9-CM 799 “Other
|
||
ill-defined and unknown causes of morbidity and mortality”</li>
|
||
</ul>
|
||
</div>
|
||
<div id="rules-for-condition-mapping" class="section level2">
|
||
<h2>RULES FOR CONDITION MAPPING</h2>
|
||
<p>In general, Conditions are records suggesting the presence of a
|
||
disease or medical condition stated as a diagnosis, a sign or a symptom.
|
||
However, there are a lot of conditions that are not originating in the
|
||
biological function of the human body but still require medical
|
||
attention. Or they are true Conditions, but not at the time of the
|
||
recording (History of) or in the person itself (Family history of). The
|
||
mapping rules for these are as follows:</p>
|
||
<p><strong>Aftercare after procedures.</strong> Those are mapped to a
|
||
single concept 413467001 “Aftercare”, and with a second “Maps to value”
|
||
relationship to the adequate procedure. For example, ICD10CM Z47.1
|
||
“Aftercare following joint replacement surgery” maps to both 413467001
|
||
“Aftercare” and to the procedure 4189532 “Implantation of joint
|
||
prosthesis”. Note that “Aftercare” is itself not a condition, but
|
||
belongs to the Observation Domain.</p>
|
||
<p><strong>Late effects or sequelae of other conditions.</strong> If
|
||
possible, these are mapped to single concepts describing them as such
|
||
late effects. For example, ICD10CM S82.874S concept_id 45589204
|
||
“Nondisplaced pilon fracture of right tibia, sequela” is mapped to
|
||
197150 “Late effect of fracture of lower extremities”. The Domain is
|
||
Condition.</p>
|
||
<p><strong>History of a condition.</strong> These are conditions, but
|
||
not at the time of the condition_start_date. Therefore, they are mapped
|
||
to the Concept 4214956 “History of clinical finding in subject”, which
|
||
is in the Observation Domain. The condition itself is recorded through
|
||
the “Maps to value” relationship. For example, ICD10CM Z87.820
|
||
concept_id “Personal history of traumatic brain injury” maps to 4214956
|
||
“History of clinical finding in subject” and with “Maps to value”
|
||
4132546 “Traumatic brain injury”.</p>
|
||
<p><strong>Family history of a condition.</strong> These, too, have a
|
||
dual mapping to 4167217 “Family history of clinical finding” and a to
|
||
the actual condition through a “Maps to value” relationship. For
|
||
example, ICD10/ICD10CM Z80.0 concept_id 45542462 “Family history of
|
||
malignant neoplasm of digestive organs” maps to 4167217 “Family history
|
||
of clinical finding” as well as 443568 “Malignant neoplasm of the
|
||
gastrointestinal tract”.</p>
|
||
<p><strong>History of medical treatment.</strong> Similarly, these are
|
||
mapped to Observation Concept 4207283 “History of drug therapy”, and
|
||
through a “Maps to value” link to the actual therapy. For example, ICD10
|
||
Z92.0 concept_id 45605174 “Personal history of contraception” goes to
|
||
4207283 “History of drug therapy” history of drug therapy and 4027509
|
||
“Contraception”. If the exact Ingredient or Clinical/Branded Drug is
|
||
known, the map would direct to these Drug Concepts. But that is not
|
||
typical.</p>
|
||
<p><strong>Adverse effect of medication.</strong> If possible, these are
|
||
mapped to a direct equivalent. However, that usually does not exist, and
|
||
then they are treated as the above history of medical treatments. For
|
||
example, both ICD10CM T36.8X5A concept_id 45551127 “Adverse effect of
|
||
other systemic antibiotics, initial encounter” and T36.8X5D “Adverse
|
||
effect of other systemic antibiotics, subsequent encounter” map to
|
||
437191 “Antibacterial drug adverse reaction”, while ICD10CM T36.8X5S
|
||
concept_id 45560654 “Adverse effect of other systemic antibiotics,
|
||
sequela” maps to 4207283 “History of drug therapy”.</p>
|
||
<p><strong>Underdosing of medication.</strong> This information is
|
||
handled similarly to the adverse effects, and the equivalent SNOMED
|
||
concepts generally do not exist. For example, ICD10CM T36.0X6A
|
||
concept_id 45565479 “Underdosing of penicillins, initial encounter” and
|
||
T36.0X6D concept_id 45565480 “Underdosing of penicillins, subsequent
|
||
encounter” go to 40488434 “Medication dose too low”, while T36.0X6S
|
||
concept_id 45565481 “Underdosing of penicillins, sequela” points at
|
||
4207283 “History of drug therapy”.</p>
|
||
<p><strong>Status of organ absence or transplant/prosthetic
|
||
presence.</strong> Absent organs are due to a procedure having removed
|
||
them (unless they are inborn conditions, which are mapped as such).
|
||
Therefore, they are mapped to 4215685 “Past history of procedure” and
|
||
the appropriate procedure that removed the organ through a “Maps to
|
||
value” link. For example, ICD10CM Z94.0 concept_id 35225404 “Kidney
|
||
transplant status” maps to 4215685 “Past history of procedure” and
|
||
4322471 “Transplant of kidney”. Z95.5 concept_id 35225418 “Presence of
|
||
coronary angioplasty implant and graft” is pointed to 4215685 “Past
|
||
history of procedure” and 4184832 “Coronary angioplasty”.</p>
|
||
<p><strong>Pre-coordinated Concepts listing two or more semantic
|
||
components through AND or OR.</strong> These concepts are treated with
|
||
the following order of precedence:</p>
|
||
<ul>
|
||
<li>To an equivalent combination concept that is also hierarchically
|
||
well connected</li>
|
||
<li>To both components separately</li>
|
||
<li>To the most common ancestor</li>
|
||
</ul>
|
||
<p>Examples for these 3 possibilities are:</p>
|
||
<ul>
|
||
<li>ICD10 A01 concept_id 45576225 “Typhoid and paratyphoid fevers” has a
|
||
single “Maps to” relationship to 4022808 “Human typhoid AND/OR
|
||
paratyphoid fever”.</li>
|
||
<li>IC10CM F12.22 concept_id 45591098 “Cannabis dependence with
|
||
intoxication” has two “Maps to” relationships to 4052690 “Cannabis
|
||
intoxication” and 440387 “Cannabis dependence”.</li>
|
||
<li>ICD10 L02.0 concept_id 45596354 “Cutaneous abscess, furuncle and
|
||
carbuncle of face” has a single “Maps to” relationship_id to 400082007
|
||
Disorder of skin of head.</li>
|
||
</ul>
|
||
<p><strong>Maternal care.</strong> Many conditions require attention not
|
||
because of a condition of a pregnant woman but of the fetus. However,
|
||
all such conditions are being mapped to the mother anyway. For example,
|
||
ICD10 O35.6 concept_id 45567927 “Maternal care for (suspected) damage to
|
||
fetus by radiation” has two “Maps to” relationships to 199553006 “Fetus
|
||
with radiation damage” and 289908002 “pregnancy”. Both conditions are
|
||
recorded with the mother.</p>
|
||
<p><strong>Need for immunization.</strong> These Concepts are mapped to
|
||
an Observation indicating such an immunity gap. A second mapping with
|
||
the relationship_id “Maps to value” is then directed to the Condition
|
||
(represented as a SNOMED Concept) the immunization is inoculating
|
||
against. Note that it is not mapped to the vaccine itself (which would
|
||
be represented as a RxNorm Concept). For example, ICD10 Z23 concept_id
|
||
45556822 “Need for immunization against single bacterial diseases” maps
|
||
to 170536002 “Vaccination required” and maps to value 87628006
|
||
“Bacterial infectious disease”.</p>
|
||
<p><strong>Conditions indicating abnormal levels of a test.</strong>
|
||
These are split into the Measurement and result Concepts. For example,
|
||
ICD10 R77.1 concept_id 45553745 “Abnormality of globulin” has a “Maps
|
||
to” relationship to the Measurement 4353510 “Globulin measurement” and a
|
||
“Maps to value” relationship to 4135493 “Abnormal”.</p>
|
||
<p><strong>Conditions resulting from the use of Devices.</strong>
|
||
Adverse or other outcomes of the exposure to a device are mapped to
|
||
473023007 “Complication associated with device and with another”Maps to
|
||
value” relationship to the device itself, if possible. For example,
|
||
ICD10 Y73.0 concept_id 45590664 “Gastroenterology and urology devices
|
||
associated with adverse incidents, diagnostic and monitoring devices”
|
||
has a “Maps to value” link to 45767866 “Gastro-urological device”.</p>
|
||
</div>
|
||
<div id="condition-mapping-algorithm" class="section level2">
|
||
<h2>CONDITION MAPPING ALGORITHM</h2>
|
||
<p><img src="images/mapping_of_concepts.png" /></p>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
</div>
|
||
</div>
|
||
|
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|
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|
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