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@jinwooyoon
jinwooyoon committed Oct 10, 2023
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720 changes: 720 additions & 0 deletions docs/Approach.html
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204 changes: 22 additions & 182 deletions docs/background.html
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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-1.13.2/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>
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<style type="text/css">

#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}

@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}

.toc-content {
padding-left: 30px;
padding-right: 40px;
}

div.main-container {
max-width: 1200px;
}

div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}

@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}

@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
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.tocify ul, .tocify li {
line-height: 20px;
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font-size: 0.90em;
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</style>



</head>

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<div class="container-fluid main-container">


<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>

<div class="toc-content col-xs-12 col-sm-8 col-md-9">




<div class="navbar navbar-default navbar-fixed-top" role="navigation">
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Background
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<li>
<a href="Approach.html">
<span class="fa fa-cogs"></span>

Approach

<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="conventions.html">
<span class="fa fa-gavel"></span>

Conventions
</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
Expand All @@ -388,61 +288,30 @@ <h1 class="title toc-ignore"><img src="images/ohdsi40x40.png"></img>Background</
</div>


<div id="problem-space-and-goals" class="section level1">
<h1><strong>Problem Space and Goals</strong></h1>
<p>test</p>
<p>The Medical Imaging Working Group (MI WG) for the OHDSI community was
formed in 2021, comprised of imaging research scientists and
observational health researchers familiar with OMOP CDM. The working
group evaluated standard vocabularies, defined fields containing key
imaging events, and identified limitations of the model. The working
group started with the R-CDM in the development of the medical imaging
extension. Imaging researchers across the field were consulted to gather
requirements and gain insights into the structure and usability of the
proposed model. The principal clinical use case focused on longitudinal
tracking of multiple lung nodules. Important attributes included CT
acquisition parameters, nodule diameter, location, density, shape, and
other phenotypes. A prototype using CT lung nodules was developed and
demonstrated at the 2023 Society of Imaging Informatics in Medicine
(SIIM) conference Hackathon.</p>
<p><br> <br></p>
<hr />
</div>
<div id="onramp" class="section level1">
<h1><strong>Onramp </strong></h1>
<p><br></p>
<div id="ohdsi-scope" class="section level3">
<h3>OHDSI Scope</h3>
<ul>
<li>test2
<ul>
<li>include SOS diagram</li>
</ul></li>
<li>medical image
<ul>
<li>Incidence, survival</li>
<li>Treatment practices</li>
<li>Safety</li>
</ul></li>
</ul>
<p><br></p>
</div>
<div id="oncology-use-cases" class="section level3">
<h3>Oncology Use Cases</h3>
<ul>
<li>TODO</li>
</ul>
<p><br></p>
</div>
<div id="data-sources" class="section level3">
<h3>Data Sources</h3>
<ul>
<li>add
<ul>
<li>Required</li>
<li>Optional</li>
</ul></li>
</ul>
<p><br></p>
</div>
<div id="test4" class="section level3">
<h3>test4</h3>
<ul>
<li>Manual curation</li>
<li>NLP</li>
</ul>
</div>
</div>
<p>Citation: Park C, You SC, Jeon H, Jeong CW, Choi JW, Park RW.
Development and Validation of the Radiology Common Data Model (R-CDM)
for the International Standardization of Medical Imaging Data. Yonsei
Med J. 2022;63(Suppl):S74. <a href="doi:10.3349/ymj.2022.63.S74"
class="uri">doi:10.3349/ymj.2022.63.S74</a></p>



</div>
</div>

</div>

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<script>
$(document).ready(function () {

// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')

// move toc-ignore selectors from section div to header
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.children('h1,h2,h3,h4,h5').addClass('toc-ignore');

// establish options
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return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
};
options.showAndHide = false;
options.smoothScroll = true;

// tocify
var toc = $("#TOC").tocify(options).data("toc-tocify");
});
</script>

<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
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Background
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<li>
<a href="Approach.html">
<span class="fa fa-cogs"></span>

Approach

<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="conventions.html">
<span class="fa fa-gavel"></span>

Conventions
</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
Expand All @@ -309,14 +291,45 @@ <h1 class="title toc-ignore"><img src="images/ohdsi40x40.png"></img>

<div id="mission" class="section level2">
<h2><strong>Mission</strong></h2>
<p>The OHDSI Image Working Group aims to provide a foundation for
representing medical imaging data within the OMOP CDM</p>
<p>The OHDSI Medical Imaging Working Group aims to represent medical
imaging data in the OMOP CDM. The differing formats between EHR and
imaging data have led to difficult to conduct research across these data
sources. Researchers using EHR data often have access to the disease
burden or patient outcomes common in medical records, while imaging
researchers can study biomarkers and granular changes in diseases that
are provided by medical imaging. Combining these sources will enable
more holistic reproducible research. Our aim is to link algorithmically
generated measurements into the OMOP data model to harness these deeper
phenotypes with the outcome measures tracked in the EHR.</p>
<p>We propose two new tables to the OMOP CDM, the medical imaging
extension model. Park et al. (2022) developed the first OMOP imaging
extension for radiological imaging studies (R-CDM). We are expanding the
R-CDM to MI-CDM to encompass diverse medical specialties and enhance
tracking provenance of the DICOM images and features.</p>
<p>Citation: Park C, You SC, Jeon H, Jeong CW, Choi JW, Park RW.
Development and Validation of the Radiology Common Data Model (R-CDM)
for the International Standardization of Medical Imaging Data. Yonsei
Med J. 2022;63(Suppl):S74. <a href="doi:10.3349/ymj.2022.63.S74"
class="uri">doi:10.3349/ymj.2022.63.S74</a></p>
<p><img
src="https://github.com/OHDSI/ImageWG/assets/84831718/e59d4692-4e41-43b2-89f7-40e9dbee74d6" /></p>
<hr />
</div>
<div id="important-links" class="section level2">
<h2><strong>Important links</strong></h2>
<p><a
href="https://www.ohdsi.org/wp-content/uploads/2023/02/OHDSI_Imaging_2023_02.pdf">Medical
Imaging Working Group 2023 OKR</a></p>
<p><a href="https://github.com/OHDSI/ImageWG/">Github Page</a></p>
<p>Paper on medical imaging OMOP CDM extension coming soon.</p>
<hr />
</div>
<div id="get-involved" class="section level2">
<h2><strong>Get Involved</strong></h2>
<p>We communicate and coordinate through the OHDSI MS Teams environment
and Github.</p>
<p>We have working group meeting every 2 weeks at 7 PM ET and 7 AM ET
alternatively. We welcome you to join us.</p>
<p><strong>MS Teams</strong></p>
<p>To join the MS Teams environment you need to complete two steps:</p>
<table>
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