docs/docs/assays.hande.html
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<main role="main">
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<p>
<a href="index.html">CIDC Documentation</a>
</p>
<h1>
H&E Assay
</h1>
<p>
<b>Description:</b> H & E assay
</p>
</div>
<div class="container">
<div class="accordion" id="assay_accordion">
<div class="card">
<div class="card-header" id="assay_metadata">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_metadata_card" aria-expanded="false" aria-controls="assay_metadata_card">
Assay Metadata
</button>
</h2>
</div>
<div id="assay_metadata_card" class="collapse" aria-labelledby="assay_metadata" data-parent="#assay_accordion">
<div class="card-body">
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="assay_creator">
assay_creator
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Indicates what site is filling out the assay.
</td>
<td>
<
string
>
<ul>
<li>"DFCI"</li>
<li>"Mount Sinai"</li>
<li>"Stanford"</li>
<li>"MD Anderson"</li>
<li>"Adaptive"</li>
<li>"Broad"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="protocol_identifier">
protocol_identifier
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Trial identifier used by lead organization, ie. Center for Experimental Therapeutics Program (CTEP) ID or Industry Sponsored ID. This is usually a short identifier. Example: E4412.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="assay_data">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_data_card" aria-expanded="false" aria-controls="assay_data_card">
Assay Data
</button>
</h2>
</div>
<div id="assay_data_card" class="collapse" aria-labelledby="assay_data" data-parent="#assay_accordion">
<div class="card-body">
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="records_accordion">
<div class="card">
<div class="card-header" id="records">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#records_card" aria-expanded="false" aria-controls="records_card">
records
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="records_card" class="collapse" aria-labelledby="records">
<div class="card-body">
A single data record from H & E assay.
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="cimac_id">
cimac_id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as CTTTPPPSS.AA for trial code TTT, participant PPP, sample SS, and aliquot AA.
</td>
<td>
<
string
>
as regex <br> <code>^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$</code>
</td>
</tr>
<tr>
<td>
<span id="comment">
comment
</span>
</td>
<td width=55%>
A text comment regarding this slide.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="fibrosis_percentage">
fibrosis_percentage
</span>
</td>
<td width=55%>
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="necrosis_percentage">
necrosis_percentage
</span>
</td>
<td width=55%>
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="tumor_tissue_percentage">
tumor_tissue_percentage
</span>
</td>
<td width=55%>
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="viable_stroma_percentage">
viable_stroma_percentage
</span>
</td>
<td width=55%>
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="viable_tumor_percentage">
viable_tumor_percentage
</span>
</td>
<td width=55%>
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="files_accordion">
<div class="card">
<div class="card-header" id="files">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#files_card" aria-expanded="false" aria-controls="files_card">
files
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
object
>
</div>
</div>
<div id="files_card" class="collapse" aria-labelledby="files">
<div class="card-body">
H & E assay input files.
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="image_file">
image_file
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
</td>
<td>
<
any of
>
<ul>
<li>
<a href="files.image.html">
image
</a>
</li>
<li>
<a href="files.jpg.html">
jpg
</a>
</li>
</ul>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="assay_uploads">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_uploads_card" aria-expanded="false" aria-controls="assay_uploads_card">
Assay Uploads
</button>
</h2>
</div>
<div id="assay_uploads_card" class="collapse" aria-labelledby="assay_uploads" data-parent="#assay_accordion">
<div class="card-body">
<table class="table table-striped">
<thead>
<tr>
<th>Entity</th>
<th>Description</th>
</tr>
</thead>
<tr>
<td width=25%>
<a href='assays.hande.hande_template.html'>
H & E assay template
</a>
</td>
<td>
Hemotoxylin and Eosin staining (H&E) submission.
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
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