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<div id="content">
<h1 class="title">COVID-19 PubSeq (part 6)</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge6aea9e">1. Generating output for EBI</a></li>
<li><a href="#org95e5e17">2. Defining the EBI study</a></li>
<li><a href="#org9181a73">3. Define the EBI sample</a></li>
<li><a href="#orga29cad0">4. Define the EBI sequence</a></li>
</ul>
</div>
</div>
<div id="outline-container-orge6aea9e" class="outline-2">
<h2 id="orge6aea9e"><span class="section-number-2">1</span> Generating output for EBI</h2>
<div class="outline-text-2" id="text-1">
<p>
Would it not be great an uploader to PubSeq also can export samples
to, say, EBI? That is what we discuss in this section. The submission
process is somewhat laborious and when you have submitted to PubSeq
why not export the same to EBI too with the least amount of effort?
</p>
<p>
COVID-19 PubSeq is a data source - both sequence data and metadata -
that can be used to push data to other sources, such as EBI. You can
register <a href="https://ena-docs.readthedocs.io/en/latest/submit/samples/programmatic.html">samples programmatically</a> with a specific XML interface. Note
that (at this point) if you want to submit a sequence (FASTA) it can
only be done through the <a href="https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html">Webin-CLI</a>. Raw data (FASTQ) can go through
the XML interface.
</p>
<p>
EBI sequence resources are presented through ENA. For example
<a href="https://www.ebi.ac.uk/ena/browser/view/MT394864">Sequence: MT394864.1</a>.
</p>
<p>
EBI has XML Formats for
</p>
<ul class="org-ul">
<li>SUBMISSION</li>
<li>STUDY</li>
<li>SAMPLE</li>
<li>EXPERIMENT</li>
<li>RUN</li>
<li>ANALYSIS</li>
<li>DAC</li>
<li>POLICY</li>
<li>DATASET</li>
<li>PROJECT</li>
</ul>
<p>
with the schemas listed <a href="ftp://ftp.ebi.ac.uk/pub/databases/ena/doc/xsd/sra_1_5/">here</a>. Since we are submitting sequences we
should follow submitting <a href="https://ena-docs.readthedocs.io/en/latest/submit/assembly.html">full genome assembly guidelines</a> and
<a href="https://ena-docs.readthedocs.io/en/latest/submit/general-guide/programmatic.html">ENA guidelines</a>. The first step is to define the study, next the sample
and finally the sequence (assembly).
</p>
</div>
</div>
<div id="outline-container-org95e5e17" class="outline-2">
<h2 id="org95e5e17"><span class="section-number-2">2</span> Defining the EBI study</h2>
<div class="outline-text-2" id="text-2">
<p>
A study is defined <a href="https://ena-docs.readthedocs.io/en/latest/submit/study/programmatic.html">here</a> and looks like
</p>
<div class="org-src-container">
<pre class="src src-xml"><PROJECT_SET>
<PROJECT alias="COVID-19 Washington DC">
<TITLE>Sequencing SARS-CoV-2 in the Washington DC area</TITLE>
<DESCRIPTION>This study collects samples from COVID-19 patients in the Washington DC area</DESCRIPTION>
<SUBMISSION_PROJECT>
<SEQUENCING_PROJECT/>
</SUBMISSION_PROJECT>
</PROJECT>
</PROJECT_SET>
</pre>
</div>
<p>
also a submission 'command' is required looking like
</p>
<div class="org-src-container">
<pre class="src src-xml"><SUBMISSION>
<ACTIONS>
<ACTION>
<ADD/>
</ACTION>
<ACTION>
<HOLD HoldUntilDate="TODO: release date"/>
</ACTION>
</ACTIONS>
</SUBMISSION>
</pre>
</div>
<p>
The webin system accepts such sources using a command like
</p>
<pre class="example">
curl -u username:password -F "SUBMISSION=@submission.xml" \
-F "PROJECT=@project.xml" "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/"
</pre>
<p>
as described <a href="https://ena-docs.readthedocs.io/en/latest/submit/study/programmatic.html#submit-the-xmls-using-curl">here</a>. Note that this is the test server. For the final
version use www.ebi.ac.uk instead of wwwdev.ebi.ac.uk. You may also
need the –insecure switch to circumvent certificate checking.
</p>
<p>
<i>work in progress (WIP)</i>
</p>
</div>
</div>
<div id="outline-container-org9181a73" class="outline-2">
<h2 id="org9181a73"><span class="section-number-2">3</span> Define the EBI sample</h2>
<div class="outline-text-2" id="text-3">
<p>
<i>work in progress (WIP)</i>
</p>
</div>
</div>
<div id="outline-container-orga29cad0" class="outline-2">
<h2 id="orga29cad0"><span class="section-number-2">4</span> Define the EBI sequence</h2>
<div class="outline-text-2" id="text-4">
<p>
<i>work in progress (WIP)</i>
</p>
</div>
</div>
</div>
<div id="postamble" class="status">
<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-17 Fri 06:05</small>.
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