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Add documentation for grade
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kzollove committed Jan 24, 2024
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84 changes: 68 additions & 16 deletions docs/conventions.html
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<title>Oncology Conventions</title>
<title>conventions.knit</title>

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<h1 class="title toc-ignore"><img src="images/ohdsi40x40.png"></img>Oncology
Conventions</h1>
<h1 class="title toc-ignore"><div>
<img src="images/ohdsi40x40.png"></img>Oncology Conventions
</div></h1>

</div>

Expand Down Expand Up @@ -756,26 +764,70 @@ <h4>Usage</h4>
<div id="grading" class="section level3 tabset tabset-fade">
<h3 class="tabset tabset-fade">Grading</h3>
<blockquote>
<p><svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:orange;overflow:visible;position:relative;"><path d="M256 32c14.2 0 27.3 7.5 34.5 19.8l216 368c7.3 12.4 7.3 27.7 .2 40.1S486.3 480 472 480H40c-14.3 0-27.6-7.7-34.7-20.1s-7-27.8 .2-40.1l216-368C228.7 39.5 241.8 32 256 32zm0 128c-13.3 0-24 10.7-24 24V296c0 13.3 10.7 24 24 24s24-10.7 24-24V184c0-13.3-10.7-24-24-24zm32 224a32 32 0 1 0 -64 0 32 32 0 1 0 64 0z"/></svg>
Under Construction</p>
<p><svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:green;overflow:visible;position:relative;"><path d="M256 48a208 208 0 1 1 0 416 208 208 0 1 1 0-416zm0 464A256 256 0 1 0 256 0a256 256 0 1 0 0 512zM369 209c9.4-9.4 9.4-24.6 0-33.9s-24.6-9.4-33.9 0l-111 111-47-47c-9.4-9.4-24.6-9.4-33.9 0s-9.4 24.6 0 33.9l64 64c9.4 9.4 24.6 9.4 33.9 0L369 209z"/></svg>
Complete</p>
</blockquote>
<blockquote>
<p><svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M256 512A256 256 0 1 0 256 0a256 256 0 1 0 0 512zM216 336h24V272H216c-13.3 0-24-10.7-24-24s10.7-24 24-24h48c13.3 0 24 10.7 24 24v88h8c13.3 0 24 10.7 24 24s-10.7 24-24 24H216c-13.3 0-24-10.7-24-24s10.7-24 24-24zm40-208a32 32 0 1 1 0 64 32 32 0 1 1 0-64z"/></svg>
Condition Modifier</p>
</blockquote>
<div id="description-3" class="section level4">
<h4>Description</h4>
<p>Abcdefg</p>
<p>Map directly to the concepts in the Cancer Modifier vocabulary. The
standard concepts for grade are broken down into 1-4 as well as High,
Intermediate, and Low.</p>
<p>A few specific grading systems (e.g. Nottingham, FIGO) are
represented as standard concepts in the Cancer Modifier vocabulary. Map
to these concepts if they match the granularity of your data. If you
have a specific need for a different grading system, you can request
that it be standardized by <a
href="https://github.com/OHDSI/OncologyWG/issues/new?assignees=&amp;labels=&amp;projects=&amp;template=issue-.md&amp;title=">creating
an issue</a>.</p>
<hr />
</div>
<div id="mapping-3" class="section level4">
<h4>Mapping</h4>
<p>HIJKLM</p>
<p>For example: Grade 1</p>
<p>Above: Any tumor that has been assigned a Grade 1 in any grading
system</p>
<p>To find the correct standard concept, you need to join to the concept
code, as shown here:</p>
<pre class="sql"><code>SELECT concept_id
FROM concept
WHERE vocabulary_id = &#39;Cancer Modifier&#39;
AND concept_class_id = &#39;Staging/Grading&#39;
AND standard_concept = &#39;S&#39;
AND concept_code = &#39;Grade-1&#39;</code></pre>
<p>Another example: Gleason Score 8</p>
<p>Above: A tumor assigned a Gleason Score of 8 using the Gleason
grading system</p>
<p>To find the correct standard concept, you need to join to the concept
code, as shown here:</p>
<pre class="sql"><code>SELECT concept_id
FROM concept
WHERE vocabulary_id = &#39;Cancer Modifier&#39;
AND concept_class_id = &#39;Staging/Grading&#39;
AND standard_concept = &#39;S&#39;
AND concept_code = &#39;Gleason-Score-8&#39;</code></pre>
<hr />
</div>
<div id="usage-3" class="section level4">
<h4>Usage</h4>
<p>NOPQ</p>
<p>To find all standard Grade concepts in the Cancer Modifier
vocabulary:</p>
<pre class="sql"><code>SELECT b.concept_id, b.concept_code, b.concept_name
FROM (
SELECT *
FROM concept c
INNER JOIN concept_ancestor ca
ON c.concept_id = ca.ancestor_concept_id
WHERE vocabulary_id = &#39;Cancer Modifier&#39;
AND concept_class_id = &#39;Staging/Grading&#39;
AND standard_concept = &#39;S&#39;
AND lower(concept_code) LIKE &#39;%grade%&#39;
) a
INNER JOIN concept b
ON a.descendant_concept_id = b.concept_id</code></pre>
<hr />
</div>
</div>
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30 changes: 19 additions & 11 deletions docs/development.html
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<title> Development Overview</title>
<title>development.knit</title>

<script src="site_libs/header-attrs-2.25/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.15/header-attrs.js"></script>
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<h1 class="title toc-ignore"><img src="images/ohdsi40x40.png"></img>
Development Overview</h1>
<h1 class="title toc-ignore"><div>
<img src="images/ohdsi40x40.png"></img> Development Overview
</div></h1>

</div>

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30 changes: 19 additions & 11 deletions docs/genomics.html
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<title> Genomics</title>
<title>genomics.knit</title>

<script src="site_libs/header-attrs-2.25/header-attrs.js"></script>
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<h1 class="title toc-ignore"><img src="images/ohdsi40x40.png"></img>
Genomics</h1>
<h1 class="title toc-ignore"><div>
<img src="images/ohdsi40x40.png"></img> Genomics
</div></h1>

</div>

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<title> Getting Involved</title>
<title>gettingInvolved.knit</title>

<script src="site_libs/header-attrs-2.25/header-attrs.js"></script>
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<h1 class="title toc-ignore"><img src="images/ohdsi40x40.png"></img>
Getting Involved</h1>
<h1 class="title toc-ignore"><div>
<img src="images/ohdsi40x40.png"></img> Getting Involved
</div></h1>

</div>

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