docs/docs/assays.olink.html
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<p>
<a href="index.html">CIDC Documentation</a>
</p>
<h1>
Olink Assay
</h1>
<p>
<b>Description:</b> High-throughput multiplexed assays for protein biomarker discovery.
</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="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>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="batches_accordion">
<div class="card">
<div class="card-header" id="batches">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#batches_card" aria-expanded="false" aria-controls="batches_card">
batches
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="batches_card" class="collapse" aria-labelledby="batches">
<div class="card-body">
<br>
<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="batch_id">
batch_id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
A unique identifier for this Olink upload
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="panel">
panel
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Panel used for the assay.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="assay_panel_lot">
assay_panel_lot
</span>
</td>
<td width=55%>
Lot number of the assay panel.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="combined_accordion">
<div class="card">
<div class="card-header" id="combined">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#combined_card" aria-expanded="false" aria-controls="combined_card">
combined
</button>
<div style="float: right;">
<
object
>
</div>
</div>
<div id="combined_card" class="collapse" aria-labelledby="combined">
<div class="card-body">
Batch-level combined NPX file.
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="npx_file">
npx_file
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about an NPX file.
</td>
<td>
<a href="files.npx.html">
npx
</a>
</td>
</tr>
<tr>
<td>
<span id="npx_manager_version">
npx_manager_version
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Version of NPX manager used for the analysis.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="study_accordion">
<div class="card">
<div class="card-header" id="study">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#study_card" aria-expanded="false" aria-controls="study_card">
study
</button>
<div style="float: right;">
<
object
>
</div>
</div>
<div id="study_card" class="collapse" aria-labelledby="study">
<div class="card-body">
Study-level combined NPX file.
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="npx_file">
npx_file
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about an NPX file.
</td>
<td>
<a href="files.npx.html">
npx
</a>
</td>
</tr>
<tr>
<td>
<span id="npx_manager_version">
npx_manager_version
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Version of NPX manager used for the analysis.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</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="batches_accordion">
<div class="card">
<div class="card-header" id="batches">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#batches_card" aria-expanded="false" aria-controls="batches_card">
batches
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="batches_card" class="collapse" aria-labelledby="batches">
<div class="card-body">
<br>
<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 Olink 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="npx_manager_version">
npx_manager_version
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Version of NPX manager used for the analysis.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="number_of_samples">
number_of_samples
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Number of samples analyzed in the assay.
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="baseline_correction">
baseline_correction
</span>
</td>
<td width=55%>
Method used for baseline correction.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="chip_barcode">
chip_barcode
</span>
</td>
<td width=55%>
Chip barcode number.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="fludigm_application_build">
fludigm_application_build
</span>
</td>
<td width=55%>
Build of the Fluidgm application used.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="fludigm_application_version">
fludigm_application_version
</span>
</td>
<td width=55%>
Version of the Fluidgm application used.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="instrument">
instrument
</span>
</td>
<td width=55%>
Instrument used for the Olink assay.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="number_of_samples_failed">
number_of_samples_failed
</span>
</td>
<td width=55%>
Number of samples failed in the assay.
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="passive_reference">
passive_reference
</span>
</td>
<td width=55%>
Passive Reference.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="probe_type">
probe_type
</span>
</td>
<td width=55%>
Probe Type.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="quality_threshold">
quality_threshold
</span>
</td>
<td width=55%>
Threshold used for quality cutoff.
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="run_date">
run_date
</span>
</td>
<td width=55%>
Date when the Olink assay was run.
</td>
<td>
<
string
: date
>
</td>
</tr>
<tr>
<td>
<span id="run_time">
run_time
</span>
</td>
<td width=55%>
Time when the Olink assay was run.
</td>
<td>
<
string
: time
>
</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">
Olink 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="assay_npx">
assay_npx
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about an NPX file.
</td>
<td>
<a href="files.npx.html">
npx
</a>
</td>
</tr>
<tr>
<td>
<span id="assay_raw_ct">
assay_raw_ct
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a comma separated file.
</td>
<td>
<a href="files.csv.html">
csv
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</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.olink.olink_template.html'>
Olink assay template
</a>
</td>
<td>
Olink proteomics submission.
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
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