757 lines
21 KiB
HTML
757 lines
21 KiB
HTML
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<a href="background.html">Model Background</a>
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<h1 class="title toc-ignore"><strong>Custom Concepts</strong></h1>
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</div>
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<p><em>By Maxim Moinat and the Themis Working Group</em></p>
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<p>The Themis Working Group convened on October 6th and December 7th
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2023 to discuss the creation this convention for creating custom
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concepts.</p>
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<div id="introduction" class="section level2">
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<h2>Introduction</h2>
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<p>While the OMOP vocabularies are very comprehensive, it is not always
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possible to use concepts existing in the OMOP vocabularies. For example,
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when using a vocabulary that is only used in your institution or having
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custom defined variables. In these cases, custom concepts can be used.
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Custom concepts are concepts that are not part of the OMOP vocabularies,
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and are only used in your institution. There are two main reasons to
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define custom concepts in your local OMOP CDM vocabulary. The first is
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that they are available in your local Atlas instance, which has several
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use cases:</p>
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<ul>
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<li>When viewing a standard concept, you can see which custom concepts
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are mapped to it. This allows you to better understand what the standard
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concept represents in your institution.</li>
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<li>You can search for a custom concept and find which standard concepts
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it is mapped to, to include in your standard concept set.</li>
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<li>For studies only using your local data, you can define cohorts using
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custom concepts (through ‘Add attribute’->‘Add … Source
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Concept’).</li>
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</ul>
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<p>The second reason is using the custom concepts in your ETL. By
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creating both the custom concept, and the ‘Maps to’ relationship
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(example below), we can use this in the same way as mapping other source
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vocabularies.</p>
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<p><strong>Custom concepts are only defined locally. These cannot be
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used for network research. Therefore it remains very important to map to
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standard concepts.</strong></p>
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</div>
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<div id="conventions" class="section level2">
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<h2>Conventions</h2>
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<p>It is important to follow a set of conventions when creating custom
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concepts, to avoid negatively impacting network studies. The conventions
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are as follows:</p>
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<ul>
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<li>Custom concepts have a <code>concept_id</code> larger than
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2,000,000,000. This is to avoid clashes with existing
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concepts.<sup>†</sup></li>
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<li>Custom concepts are always non-standard
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(<code>concept.standard_concept = NULL</code>).</li>
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<li>Custom concepts can only be used in the
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<code>_source_concept_id</code> fields
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(e.g. <code>procedure_source_concept_id</code>)</li>
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<li>If the field <code>_source_concept_id</code> does not exist, add a
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custom column to your table (e.g. a
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<code>drug_exposure.route_source_concept_id</code>)<sup>1</sup>. If
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there is a wide need in the community, a proposal can be submitted to
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the CDM Working Group to add these fields in a future OMOP CDM
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version.</li>
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<li>Always add custom concepts to a new vocabulary specifically for your
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source (see example below). If you have a need to add concepts to an
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existing vocabulary, please contact the OHDSI Vocabulary Working
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Group.</li>
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<li>Do NOT add custom concepts to the hierarchy of existing vocabularies
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(either in the <code>concept_ancestor</code> table or
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<code>subsumes</code>/<code>is a</code> relations in the
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<code>concept_relationship</code> table). This is to avoid descendant
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concepts to differ between sites.</li>
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</ul>
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<p>In addition, it is recommended to follow these suggestions:</p>
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<ul>
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<li>For the <code>domain_id</code>, choose an appropriate existing value
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from the domain table (‘Condition’, ‘Drug’, ‘Procedure’, etc.). Note
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that this determines the target table the concept can be used in.</li>
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<li>For the <code>concept_class_id</code>, it is not required to create
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new classes for your source vocabulary. To leave the class empty
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explicitly, use class ‘Undefined’. It is also allowed to reuse existing
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concept classes (e.g. SNOMED’s ‘Clinical Finding’ for conditions or
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RxNorm drug classes ‘Ingredient’, ‘Clinical Drug’, ‘Branded Drug’
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etc.).</li>
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<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 & 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>
|
||
</div>
|
||
|
||
|
||
|
||
|
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</div>
|
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