Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add documentation for grade #632

Merged
merged 2 commits into from
Jan 24, 2024
Merged

Add documentation for grade #632

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
f448d38
Add documentation for grade
kzollove Jan 24, 2024
1fcdb61
Render HTML docs
github-actions[bot] Jan 24, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
54 changes: 49 additions & 5 deletions docs/conventions.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -756,26 +756,70 @@ <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>
Expand Down
Loading