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rtmill committed Jan 11, 2024
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<title>background.knit</title>
<title> Background</title>

<script src="site_libs/header-attrs-2.15/header-attrs.js"></script>
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<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
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border-radius: 4px;
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Conventions
</a>
</li>
<li>
<a href="model.html">
<span class="fa fa-sitemap"></span>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-people-group"></span>

Model
</a>
</li>
<li>
<a href="tooling.html">
<span class="fa fa-wrench"></span>
Implementation

Tools
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="model.html">
<span class="fa fa-sitemap"></span>

Model
</a>
</li>
<li>
<a href="installation.html">
<span class="fa fa-sitemap"></span>

Installation
</a>
</li>
<li>
<a href="tooling.html">
<span class="fa fa-wrench"></span>

Tools
</a>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-people-group"></span>

ETLs
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="naaccr.html">
<span class="fa fa-sitemap"></span>

NAACCR
</a>
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</ul>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
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<h1 class="title toc-ignore"><div>
<img src="images/ohdsi40x40.png"></img> Background
</div></h1>
<h1 class="title toc-ignore"><img src="images/ohdsi40x40.png"></img>
Background</h1>

</div>


<p><br></p>
<div id="problem-space" class="section level1">
<h1><strong>Problem Space</strong></h1>
<p>In a typical observational study, the definition of the study
population (cohort), exposures and outcomes are usually based on
diagnostic codes in addition to drug exposures, procedure occurrences or
lab measurements. For cancer studies, this information is typically not
sufficient, as more details are required for the proper identification
of the study population, treatment and subsequent outcomes.</p>
<p>Appropriate characterization of cancer requires details such as
anatomical site, morphology, local penetration, affected lymph nodes,
metastatic spread, biomarkers, and disease staging and grading. In
typical observational data sources, this necessary level of detail is
not regularly present. Patient results from diagnostic procedures are
collected but may not be available within the given data source or what
is collected cannot appropriately serve as a surrogate for the above
attributes. Correct identification of cancer treatment regimens also
tends to be more complex compared to other disease modalities within
observational data. Most cancer treatments are administered in
chemotherapy regimens with complex dosing and scheduling in multiple
cycles and are often combined with targeted therapies, immunotherapies,
surgery or radiotherapy. None of these attributes follow standard
definition to be applied to observational data, as most regimens are
personalized to the individual patient need, making a priori
standardized definitions more complex. Additionally, clinically relevant
information on disease, treatment and outcomes that appropriately
reflects a patient’s journey including information on the time of
diagnosis, response to treatments, time to treatment failure, disease
progression, recurrence and (disease-free and overall) survival requires
data abstraction and is rarely available in the source data and has not
been traditionally supported in OMOP CDM.</p>
<p>The Oncology CDM Extension of the OMOP CDM aims to provide a
foundation for representing cancer data at the levels of granularity and
abstraction required to support observational cancer research.</p>
<p>The extension has been tested in EHR and Cancer Registry data against
a number of typical use cases.</p>
<hr />
</div>
<div id="goals" class="section level1">
<h1><strong>Goals</strong></h1>
<p>The overarching goals of the OHDSI Oncology Working Group:</p>
<p><br></p>
<div id="oncology-research" class="section level3">
<h3>1) Oncology research</h3>
<ul>
<li>Enabling</li>
<li>Conducting</li>
<li>Promoting</li>
</ul>
</div>
<div id="maturing-oncology-standards" class="section level3">
<h3>2) Maturing oncology standards</h3>
<ul>
<li>Data model, ontologies and conventions</li>
<li>A shared, international oncology data standard</li>
<li>Support of observational, claims and curated data sources</li>
</ul>
</div>
<div id="community-growth" class="section level3">
<h3>3) Community growth</h3>
<ul>
<li>Model adoption and growth of network</li>
<li>Data holders, developers, and subject matter experts</li>
<li>Research use cases and applications</li>
</ul>
</div>
<div id="transparency" class="section level3">
<h3>4) Transparency</h3>
<ul>
<li>Clear processes and mechanisms for collaboration</li>
<li>Thorough documentation of conventions and approaches</li>
<li>Open-source development and project management</li>
</ul>
<p><br></p>
<hr />
</div>
</div>
<div id="notable-challenges" class="section level1">
<h1><strong>Notable Challenges</strong></h1>
<p><br></p>
<div id="oncology-data-in-omop" class="section level3">
<h3>1) Oncology data in OMOP</h3>
<ul>
<li>OMOP typically a person-centric model
<ul>
<li>Oncology data often requires additional levels of detail</li>
<li>e.g., “Observations about observations”</li>
</ul></li>
<li>Novel entity relationships in source data</li>
</ul>
<p><br></p>
</div>
<div id="source-data-representations" class="section level3">
<h3>2) Source data representations</h3>
<ul>
<li>Differing granularity and detail between data sources</li>
<li>Goal of maximum accommodation while maintaing FAIR principles</li>
<li>Sources include observational, claims and curated data
<ul>
<li>Sources often overlap and can provide complementary data for same
patient population</li>
</ul></li>
</ul>
<p><br></p>
<figure>
<p><img src="https://user-images.githubusercontent.com/57408355/76053847-9c1c5380-5f3c-11ea-8ac2-4efbcc4ee66e.png" alt="Condition Map"/></p>
<figcaption>
Diagram illustrating condition modifier representation
</figcaption>
</figure>
<p><br></p>
<hr />
</div>
</div>
<div id="publicationspresentation" class="section level1">
<h1><strong>Publications/Presentation</strong></h1>
<ul>
<li><p><a
href="https://github.com/OHDSI/OncologyWG/wiki/Oncology-Tutorial">2020
OHDSI Symposium - Oncology Tutorial</a></p></li>
<li><p><a
href="https://github.com/OHDSI/OncologyWG/wiki/Genomic-Variant-Harmonization">2020
OHDSI Symposium - Genomic Variant Harmonization Poster
Presentation</a></p></li>
<li><p><a
href="https://github.com/OHDSI/OncologyWG/wiki/Bladder-Cancer-Study">Bladder
Cancer Study</a></p></li>
<li><p><a href="https://ascopubs.org/doi/10.1200/CCI.20.00079">JCO
Clinical Cancer Informatics</a></p></li>
</ul>
<p><br></p>
</div>




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