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Merge pull request #613 from OHDSI/documentation_rehaul
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Documentation rehaul
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@rtmill
rtmill authored Oct 18, 2023
2 parents 19a95f8 + da9e245 commit 3611dab
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181 changes: 115 additions & 66 deletions docs/background.html
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<title>Background</title>
<title> Background</title>

<script src="site_libs/header-attrs-2.21/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.24/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<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>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<script src="site_libs/jqueryui-1.13.2/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-6.4.0/css/all.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.0/css/v4-shims.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />

<style type="text/css">
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<a href="index.html">
<span class="fa fa-home"></span>

Home
</a>
</li>
<li>
<a href="background.html">
<span class="fa fa-info-circle"></span>
<span class="fa fa-circle-info"></span>

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

Approach
Development Effort

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

Model
Development Overview
</a>
</li>
<li>
<a href="conventions.html">
<span class="fa fa-gavel"></span>
<a href="progressMap.html">
<span class="fa fa-list-check"></span>

Conventions
Progress Map
</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-plug"></span>

Implementation

<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="installation.html">
<span class="fa fa-download"></span>
<a href="githubProject.html">
<span class="fa fa-github"></span>

Install
Github Project Orientation
</a>
</li>
<li>
<a href="population.html">
<span class="fa fa-database"></span>
<a href="gettingInvolved.html">
<span class="fa fa-user-plus"></span>

Populate Data
Getting Involved
</a>
</li>
</ul>
</li>
<li>
<a href="conventions.html">
<span class="fa fa-gavel"></span>

Conventions
</a>
</li>
<li>
<a href="model.html">
<span class="fa fa-sitemap"></span>

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

Tooling
Tools
</a>
</li>
</ul>
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<h1 class="title toc-ignore"><img src="images/ohdsi40x40.png"></img>Background</h1>
<h1 class="title toc-ignore"><img src="images/ohdsi40x40.png"></img>
Background</h1>

</div>


<div id="problem-space-and-goals" class="section level1">
<h1><strong>Problem Space and Goals</strong></h1>
<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
Expand Down Expand Up @@ -457,56 +463,99 @@ <h1><strong>Problem Space and Goals</strong></h1>
a number of typical use cases.</p>
<hr />
</div>
<div id="onramp" class="section level1">
<h1><strong>Onramp </strong></h1>
<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="ohdsi-scope" class="section level3">
<h3>OHDSI Scope</h3>
<div id="oncology-research" class="section level3">
<h3>1) Oncology research</h3>
<ul>
<li>OHDSI Problem Space
<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>include SOS diagram</li>
</ul></li>
<li>What OMOP Oncology can do today
<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>Incidence, survival</li>
<li>Treatment practices</li>
<li>Safety</li>
</ul></li>
<li>What OMOP Oncology cannot do (without outcomes)
<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>Treatment response</li>
<li>Comparative effectiveness</li>
<li>PFS/DFS</li>
</ul></li>
<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 id="oncology-use-cases" class="section level3">
<h3>Oncology Use Cases</h3>
</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>TODO</li>
<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="data-sources" class="section level3">
<h3>Data Sources</h3>
<div id="source-data-representations" class="section level3">
<h3>2) Source data representations</h3>
<ul>
<li>what data sources do I need to get oncology value from OMOP
<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>Required</li>
<li>Optional</li>
<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="how-will-we-get-outcomes-data" class="section level3">
<h3>How will we get outcomes data?</h3>
<div id="publicationspresentation" class="section level1">
<h1><strong>Publications/Presentation</strong></h1>
<ul>
<li>Manual curation</li>
<li>NLP</li>
<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>
</div>
<p><br></p>
</div>


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// establish options
var options = {
selectors: "h1,h2,h3",
selectors: "h1,h2",
theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
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