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Merge pull request #678 from OHDSI/olympians_week3 

Info on CDM Additions
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clairblacketer 2024-04-22 17:03:59 -04:00 committed by GitHub
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40 changed files with 14605 additions and 1656 deletions
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<h1 class="title toc-ignore"><img src="ohdsi40x40.png"></img> Types of
OMOP CDM Additions</h1>
</div>
<p>While the OMOP CDM supports a diverse set of use cases and data
types, we acknowledge that not all can be represented in the CDM in its
current form. Based on your use case it may be necessary to modify just
your database, create an expansion, or suggest changes to the model that
will be incorporated into the next official version. This document
describes the types of additions that can be made to the CDM and how
they should be utilized by the community.</p>
<div id="site---specific-add-on" class="section level2">
<h2>Site - Specific Add on</h2>
<p>It is entirely within your rights as a data owner or holder to create
additional columns or even tables in your own instance of your CDM that
is specific to your site. However, they are not supported or recognized
by OHDSI tools and not part of the canonical OMOP CDM. The Add on column
or table is used for a site specific use case or data element. Examples
include: privacy flags, source table identifiers or other data elements.
See <a
href="https://www.ohdsi.org/wp-content/uploads/2021/09/18-Implementing-Adopting-a-Customized-OMOP-Common-Data-Model.pdf">this
poster</a> for background information and an implementation guide.</p>
</div>
<div id="expansionextension" class="section level2">
<h2>Expansion/Extension</h2>
<p>These are typically sets of tables created by working groups to model
a specific type of data. The idea is that these tables follow the
general conventions of the OMOP CDM but are not part of the canonical
data model and therefore do not fall under the purview of the CDM
working group. They are developed using OMOP conventions applied to
domain specific datasets. It is possible they could become part of the
CDM in the future (like the episode and episode_event tables) but that
is not a given. If using an expansion/extension with your data they are
invisible to the tools. They can be used as part of network research but
you would need to ensure that all participating databases are using the
extension/expansion before writing a study package that incorporates the
tables.</p>
<p><strong>Examples include:</strong></p>
<ul>
<li>Oncology
<ul>
<li>Github: <a href="https://ohdsi.github.io/OncologyWG/"
class="uri">https://ohdsi.github.io/OncologyWG/</a></li>
</ul></li>
<li>Medical Imaging
<ul>
<li>Github: <a href="https://github.com/paulnagy/DICOM2OMOP"
class="uri">https://github.com/paulnagy/DICOM2OMOP</a></li>
<li>Paper: <a
href="https://link-springer-com.ezjandj.infotrieve.com/article/10.1007/s10278-024-00982-6"
class="uri">https://link-springer-com.ezjandj.infotrieve.com/article/10.1007/s10278-024-00982-6</a></li>
</ul></li>
<li>GIS
<ul>
<li>Github: <a href="https://ohdsi.github.io/GIS/"
class="uri">https://ohdsi.github.io/GIS/</a></li>
</ul></li>
</ul>
</div>
<div id="cdm-addition-or-change" class="section level2">
<h2>CDM Addition or Change</h2>
<p>Please see the <a href="/cdmRequestProcess.html">full process</a> for
how to request changes to the CDM. These change requests MUST be backed
by network uses cases and MUST be approved by the CDM working group.
Overall these are typically small changes or additions that make the CDM
more usable from a network perspective or fulfill a clearly demonstrated
need. Good examples are the recently ratified <a
href="https://github.com/OHDSI/CommonDataModel/tree/NLP_Proposal_2023">NOTE_NLP
updates</a> and presentation by the vocabulary team to add <a
href="https://ohdsiorg.sharepoint.com/:v:/s/Workgroup-CommonDataModel/EcMaYjUPeSVMrmSozflBsmQBNEtPpiCJ9AfZ3QQtGHIuFg?e=UnVgIh&amp;nav=eyJyZWZlcnJhbEluZm8iOnsicmVmZXJyYWxBcHAiOiJTdHJlYW1XZWJBcHAiLCJyZWZlcnJhbFZpZXciOiJTaGFyZURpYWxvZy1MaW5rIiwicmVmZXJyYWxBcHBQbGF0Zm9ybSI6IldlYiIsInJlZmVycmFsTW9kZSI6InZpZXcifX0%3D">value_source_concept_id</a>
to measurement and observation.</p>
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<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a> <a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li> </li>
<li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li>
<li class="dropdown-submenu"> <li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Accepted</a> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Accepted Changes</a>
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<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/tree/develop">CDM version in development</a>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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</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> </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> </li>
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---
title: '<div><img src="ohdsi40x40.png"></img> Types of OMOP CDM Additions </div>'
output:
html_document:
toc: TRUE
toc_float: TRUE
---
While the OMOP CDM supports a diverse set of use cases and data types, we acknowledge that not all can be represented in the CDM in its current form. Based on your use case it may be necessary to modify just your database, create an expansion, or suggest changes to the model that will be incorporated into the next official version. This document describes the types of additions that can be made to the CDM and how they should be utilized by the community.
## Site - Specific Add on
It is entirely within your rights as a data owner or holder to create additional columns or even tables in your own instance of your CDM that is specific to your site. However, they are not supported or recognized by OHDSI tools and not part of the canonical OMOP CDM. The Add on column or table is used for a site specific use case or data element. Examples include: privacy flags, source table identifiers or other data elements. See [this poster](https://www.ohdsi.org/wp-content/uploads/2021/09/18-Implementing-Adopting-a-Customized-OMOP-Common-Data-Model.pdf) for background information and an implementation guide.
## Expansion/Extension
These are typically sets of tables created by working groups to model a specific type of data. The idea is that these tables follow the general conventions of the OMOP CDM but are not part of the canonical data model and therefore do not fall under the purview of the CDM working group. They are developed using OMOP conventions applied to domain specific datasets. It is possible they could become part of the CDM in the future (like the episode and episode_event tables) but that is not a given. If using an expansion/extension with your data they are invisible to the tools. They can be used as part of network research but you would need to ensure that all participating databases are using the extension/expansion before writing a study package that incorporates the tables.
**Examples include:**
- Oncology
- Github: https://ohdsi.github.io/OncologyWG/
- Medical Imaging
- Github: https://github.com/paulnagy/DICOM2OMOP
- Paper: https://link-springer-com.ezjandj.infotrieve.com/article/10.1007/s10278-024-00982-6
- GIS
- Github: https://ohdsi.github.io/GIS/
## CDM Addition or Change
Please see the [full process](/cdmRequestProcess.html) for how to request changes to the CDM. These change requests MUST be backed by network uses cases and MUST be approved by the CDM working group. Overall these are typically small changes or additions that make the CDM more usable from a network perspective or fulfill a clearly demonstrated need. Good examples are the recently ratified [NOTE_NLP updates](https://github.com/OHDSI/CommonDataModel/tree/NLP_Proposal_2023) and presentation by the vocabulary team to add [value_source_concept_id](https://ohdsiorg.sharepoint.com/:v:/s/Workgroup-CommonDataModel/EcMaYjUPeSVMrmSozflBsmQBNEtPpiCJ9AfZ3QQtGHIuFg?e=UnVgIh&nav=eyJyZWZlcnJhbEluZm8iOnsicmVmZXJyYWxBcHAiOiJTdHJlYW1XZWJBcHAiLCJyZWZlcnJhbFZpZXciOiJTaGFyZURpYWxvZy1MaW5rIiwicmVmZXJyYWxBcHBQbGF0Zm9ybSI6IldlYiIsInJlZmVycmFsTW9kZSI6InZpZXcifX0%3D) to measurement and observation.