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<h1 class="title toc-ignore"><strong>Custom Concepts</strong></h1>
</div>
<p><em>By Maxim Moinat and the Themis Working Group</em></p>
<p>The Themis Working Group convened on October 6th and December 7th
2023 to discuss the creation this convention for creating custom
concepts.</p>
<div id="introduction" class="section level2">
<h2>Introduction</h2>
<p>While the OMOP vocabularies are very comprehensive, it is not always
possible to use concepts existing in the OMOP vocabularies. For example,
when using a vocabulary that is only used in your institution or having
custom defined variables. In these cases, custom concepts can be used.
Custom concepts are concepts that are not part of the OMOP vocabularies,
and are only used in your institution. There are two main reasons to
define custom concepts in your local OMOP CDM vocabulary. The first is
that they are available in your local Atlas instance, which has several
use cases:</p>
<ul>
<li>When viewing a standard concept, you can see which custom concepts
are mapped to it. This allows you to better understand what the standard
concept represents in your institution.</li>
<li>You can search for a custom concept and find which standard concepts
it is mapped to, to include in your standard concept set.</li>
<li>For studies only using your local data, you can define cohorts using
custom concepts (through Add attribute-&gt;Add … Source
Concept).</li>
</ul>
<p>The second reason is using the custom concepts in your ETL. By
creating both the custom concept, and the Maps to relationship
(example below), we can use this in the same way as mapping other source
vocabularies.</p>
<p><strong>Custom concepts are only defined locally. These cannot be
used for network research. Therefore it remains very important to map to
standard concepts.</strong></p>
</div>
<div id="conventions" class="section level2">
<h2>Conventions</h2>
<p>It is important to follow a set of conventions when creating custom
concepts, to avoid negatively impacting network studies. The conventions
are as follows:</p>
<ul>
<li>Custom concepts have a <code>concept_id</code> larger than
2,000,000,000. This is to avoid clashes with existing
concepts.<sup></sup></li>
<li>Custom concepts are always non-standard
(<code>concept.standard_concept = NULL</code>).</li>
<li>Custom concepts can only be used in the
<code>_source_concept_id</code> fields
(e.g. <code>procedure_source_concept_id</code>)</li>
<li>If the field <code>_source_concept_id</code> does not exist, add a
custom column to your table (e.g. a
<code>drug_exposure.route_source_concept_id</code>)<sup>1</sup>. If
there is a wide need in the community, a proposal can be submitted to
the CDM Working Group to add these fields in a future OMOP CDM
version.</li>
<li>Always add custom concepts to a new vocabulary specifically for your
source (see example below). If you have a need to add concepts to an
existing vocabulary, please contact the OHDSI Vocabulary Working
Group.</li>
<li>Do NOT add custom concepts to the hierarchy of existing vocabularies
(either in the <code>concept_ancestor</code> table or
<code>subsumes</code>/<code>is a</code> relations in the
<code>concept_relationship</code> table). This is to avoid descendant
concepts to differ between sites.</li>
</ul>
<p>In addition, it is recommended to follow these suggestions:</p>
<ul>
<li>For the <code>domain_id</code>, choose an appropriate existing value
from the domain table (Condition, Drug, Procedure, etc.). Note
that this determines the target table the concept can be used in.</li>
<li>For the <code>concept_class_id</code>, it is not required to create
new classes for your source vocabulary. To leave the class empty
explicitly, use class Undefined. It is also allowed to reuse existing
concept classes (e.g. SNOMEDs Clinical Finding for conditions or
RxNorm drug classes Ingredient, Clinical Drug, Branded Drug
etc.).</li>
<li>In the new vocabulary record, the <code>vocabulary_concept_id</code>
can be set to 0, as this is often not used in the OMOP CDM.</li>
<li>Create mappings between custom concepts and standard concepts. This
can be done by adding rows to the <code>concept_relationship</code>
table, with the <code>Maps to</code> relation. The reverse relation,
<code>Mapped from</code>, should also be added. This allows for easy
navigation between custom and standard concepts<sup>2</sup>. The mapped
to concept should be a standard concept.</li>
<li>Officially, <code>concept_hierarchy</code> is only for standard
concepts. However, if you local use case requires this (e.g. for
selection of descendants of custom concepts), the custom concepts can be
added into their own, isolated, hierarchy.</li>
</ul>
</div>
<div id="example" class="section level2">
<h2>Example</h2>
<p>In this example, we will add one custom concept for the DHD Diagnose
Thesaurus. This is a Dutch vocabulary, which is not part of the OMOP
vocabularies. We will add the concept diabetes mellitus type 1. This
concept has a mapping to the standard concept Diabetes mellitus type 1
(disorder), concept_id 3341872.</p>
<p>After creating these records, we can use the custom concept in our
ETL to populate the <code>condition_source_concept_id</code> field.</p>
<div id="custom-vocabulary" class="section level3">
<h3>Custom vocabulary</h3>
<table>
<colgroup>
<col width="50%" />
<col width="50%" />
</colgroup>
<thead>
<tr class="header">
<th>Field</th>
<th>Value</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>vocabulary_id</td>
<td>DHD Diagnose Thesaurus</td>
</tr>
<tr class="even">
<td>vocabulary_name</td>
<td>Dutch Hospital Data Diagnosethesaurus</td>
</tr>
<tr class="odd">
<td>vocabulary_reference</td>
<td><a
href="https://www.dhd.nl/producten-diensten/diagnosethesaurus/Paginas/diagnosethesaurus.asp"
class="uri">https://www.dhd.nl/producten-diensten/diagnosethesaurus/Paginas/diagnosethesaurus.asp</a></td>
</tr>
<tr class="even">
<td>vocabulary_version</td>
<td>2023-04-20</td>
</tr>
<tr class="odd">
<td>vocabulary_concept_id</td>
<td>0</td>
</tr>
</tbody>
</table>
</div>
<div id="custom-concept" class="section level3">
<h3>Custom concept</h3>
<table>
<thead>
<tr class="header">
<th>Field</th>
<th>Value</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>concept_id</td>
<td>2 000 000 001</td>
</tr>
<tr class="even">
<td>concept_name</td>
<td>diabetes mellitus type 1</td>
</tr>
<tr class="odd">
<td>domain_id</td>
<td>Condition</td>
</tr>
<tr class="even">
<td>vocabulary_id</td>
<td>DHD Diagnose Thesaurus</td>
</tr>
<tr class="odd">
<td>concept_class_id</td>
<td>Undefined</td>
</tr>
<tr class="even">
<td>standard_concept</td>
<td><code>NULL</code></td>
</tr>
<tr class="odd">
<td>concept_code</td>
<td>0000002630</td>
</tr>
<tr class="even">
<td>valid_start_date</td>
<td>2017-08-01</td>
</tr>
<tr class="odd">
<td>valid_end_date</td>
<td>2099-12-31</td>
</tr>
<tr class="even">
<td>invalid_reason</td>
<td><code>NULL</code></td>
</tr>
</tbody>
</table>
</div>
<div id="mapping-relationship" class="section level3">
<h3>Mapping relationship</h3>
<table>
<thead>
<tr class="header">
<th>Field</th>
<th>Value</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>concept_id_1</td>
<td>2 000 000 001</td>
</tr>
<tr class="even">
<td>concept_id_2</td>
<td>3341872</td>
</tr>
<tr class="odd">
<td>relationship_id</td>
<td>Maps to</td>
</tr>
<tr class="even">
<td>valid_start_date</td>
<td>2017-08-01</td>
</tr>
<tr class="odd">
<td>valid_end_date</td>
<td>2099-12-31</td>
</tr>
<tr class="even">
<td>invalid_reason</td>
<td><code>NULL</code></td>
</tr>
<tr class="odd">
<td>Field</td>
<td>Value</td>
</tr>
<tr class="even">
<td>——-</td>
<td>——-</td>
</tr>
<tr class="odd">
<td>concept_id_1</td>
<td>3341872</td>
</tr>
<tr class="even">
<td>concept_id_2</td>
<td>2 000 000 001</td>
</tr>
<tr class="odd">
<td>relationship_id</td>
<td>Mapped from</td>
</tr>
<tr class="even">
<td>valid_start_date</td>
<td>2017-08-01</td>
</tr>
<tr class="odd">
<td>valid_end_date</td>
<td>2099-12-31</td>
</tr>
<tr class="even">
<td>invalid_reason</td>
<td><code>NULL</code></td>
</tr>
</tbody>
</table>
<p>See the <a
href="https://ohdsi.github.io/CommonDataModel/sqlScripts.html#Source_to_Standard">Source
To Standard query</a> to map a code in the source data to a standard
concept.</p>
</div>
</div>
<div id="getting-your-vocabulary-into-the-omop-vocabularies"
class="section level2">
<h2>Getting your vocabulary into the OMOP vocabularies</h2>
<p>If you think your custom concepts are useful for others, you can
submit them to the OMOP vocabularies. This could be as a supported
source vocabulary (like ICD) or a new vocabulary with standard concepts
(like LOINC). This is a separate process from the conventions described
above. Please see the <a
href="https://ohdsi.github.io/CommonDataModel/vocabRequest.html">this
support page</a>.</p>
</div>
<div id="references" class="section level2">
<h2>References</h2>
<p><sup>1</sup><a
href="https://www.ohdsi.org/2021-global-symposium-showcase-18/">Melanie
Philofsky; Implementing &amp; adopting a customized OMOP Common Data
Model; OHDSI Symposium 2021</a></p>
<p><sup>2</sup><a
href="https://www.ohdsi.org/wp-content/uploads/2020/10/Melanie-Philofsky-Philofsky-Mapping-Source-Codes-Poster.pdf">Melanie
Philofsky; Mapping Custom Source Codes to Standard Concepts: A
Comparison of Two Approaches; OHDSI Symposium 2020</a> </br>
<sup></sup>this is why custom concepts are sometimes referred to as
“2B+” or “2billionaires”.</p>
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