Preparing for EBI submission

author: Pjotr Prins 2020-07-17 12:05:53 +0100
committer: Pjotr Prins 2020-07-17 12:08:43 +0100
commit: 6ade3c1d47a83f0ed52a4efe287017b6a0fcc44e (patch)
tree: 00f28ae6d9e973098aaee08534aa8414d54a957b
parent: 4f3469e2d5395526c0376688ded4340a4834677d (diff)
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7 files changed, 486 insertions, 4 deletions
diff --git a/bh20simplewebuploader/templates/blog.html b/bh20simplewebuploader/templates/blog.html
index 823f8a1..f4c2a85 100644
--- a/bh20simplewebuploader/templates/blog.html
+++ b/bh20simplewebuploader/templates/blog.html
@@ -63,6 +63,14 @@
               We explore the Arvados command line and API
             </div>
           </div>
+          <div class="blog-table-row">
+            <div class="blog-table-cell">
+              <a href="/blog?id=using-covid-19-pubseq-part6">Prepare for uploading to EBI/ENA</a>
+            </div>
+            <div class="blog-table-cell">
+              Generate the files needed for uploading to EBI/ENA
+            </div>
+          </div>
         </div>
       </div>
     </section>
diff --git a/doc/blog/using-covid-19-pubseq-part6.html b/doc/blog/using-covid-19-pubseq-part6.html
new file mode 100644
index 0000000..278abe8
--- /dev/null
+++ b/doc/blog/using-covid-19-pubseq-part6.html
@@ -0,0 +1,393 @@
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+<head>
+<!-- 2020-07-17 Fri 06:05 -->
+<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1" />
+<title>COVID-19 PubSeq (part 6)</title>
+<meta name="generator" content="Org mode" />
+<meta name="author" content="Pjotr Prins" />
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+</style>
+<link rel="Blog stylesheet" type="text/css" href="blog.css" />
+<script type="text/javascript">
+/*
+@licstart  The following is the entire license notice for the
+JavaScript code in this tag.
+
+Copyright (C) 2012-2020 Free Software Foundation, Inc.
+
+The JavaScript code in this tag is free software: you can
+redistribute it and/or modify it under the terms of the GNU
+General Public License (GNU GPL) as published by the Free Software
+Foundation, either version 3 of the License, or (at your option)
+any later version.  The code is distributed WITHOUT ANY WARRANTY;
+without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE.  See the GNU GPL for more details.
+
+As additional permission under GNU GPL version 3 section 7, you
+may distribute non-source (e.g., minimized or compacted) forms of
+that code without the copy of the GNU GPL normally required by
+section 4, provided you include this license notice and a URL
+through which recipients can access the Corresponding Source.
+
+
+@licend  The above is the entire license notice
+for the JavaScript code in this tag.
+*/
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+ }
+/*]]>*///-->
+</script>
+</head>
+<body>
+<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">&lt;PROJECT_SET&gt;
+   &lt;PROJECT alias="COVID-19 Washington DC"&gt;
+      &lt;TITLE&gt;Sequencing SARS-CoV-2 in the Washington DC area&lt;/TITLE&gt;
+      &lt;DESCRIPTION&gt;This study collects samples from COVID-19 patients in the Washington DC area&lt;/DESCRIPTION&gt;
+      &lt;SUBMISSION_PROJECT&gt;
+         &lt;SEQUENCING_PROJECT/&gt;
+      &lt;/SUBMISSION_PROJECT&gt;
+   &lt;/PROJECT&gt;
+&lt;/PROJECT_SET&gt;
+</pre>
+</div>
+
+<p>
+also a submission 'command' is required looking like
+</p>
+
+<div class="org-src-container">
+<pre class="src src-xml">&lt;SUBMISSION&gt;
+   &lt;ACTIONS&gt;
+      &lt;ACTION&gt;
+         &lt;ADD/&gt;
+      &lt;/ACTION&gt;
+      &lt;ACTION&gt;
+         &lt;HOLD HoldUntilDate="TODO: release date"/&gt;
+      &lt;/ACTION&gt;
+   &lt;/ACTIONS&gt;
+&lt;/SUBMISSION&gt;
+
+</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 &#x2013;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>.
+</div>
+</body>
+</html>
diff --git a/doc/blog/using-covid-19-pubseq-part6.org b/doc/blog/using-covid-19-pubseq-part6.org
index 2d1c5e0..8964700 100644
--- a/doc/blog/using-covid-19-pubseq-part6.org
+++ b/doc/blog/using-covid-19-pubseq-part6.org
@@ -83,9 +83,12 @@ also a submission 'command' is required looking like
 
 The webin system accepts such sources using a command like
 
-: curl -u username:password -F "SUBMISSION=@submission.xml" -F "PROJECT=@project.xml" "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/"
+: curl -u username:password -F "SUBMISSION=@submission.xml" \
+:   -F "PROJECT=@project.xml" "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/"
 
-as described [[https://ena-docs.readthedocs.io/en/latest/submit/study/programmatic.html#submit-the-xmls-using-curl][here]].
+as described [[https://ena-docs.readthedocs.io/en/latest/submit/study/programmatic.html#submit-the-xmls-using-curl][here]]. 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.
 
 /work in progress (WIP)/
 
diff --git a/scripts/submit_ebi/example/project-submission.xml b/scripts/submit_ebi/example/project-submission.xml
index 2d3ddc1..1abb827 100644
--- a/scripts/submit_ebi/example/project-submission.xml
+++ b/scripts/submit_ebi/example/project-submission.xml
@@ -1,3 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
 <SUBMISSION>
    <ACTIONS>
       <ACTION>
@@ -6,6 +7,6 @@
       <ACTION>
          <HOLD HoldUntilDate="2020-10-10"/>
       </ACTION>
-   </ACTIONS>
+  </ACTIONS>
 </SUBMISSION>
 
diff --git a/scripts/submit_ebi/example/project.xml b/scripts/submit_ebi/example/project.xml
index 90704ab..6a817e7 100644
--- a/scripts/submit_ebi/example/project.xml
+++ b/scripts/submit_ebi/example/project.xml
@@ -1,7 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
 <PROJECT_SET>
    <PROJECT alias="PubSeq01">
       <TITLE>Testing PubSeq Sample uploads</TITLE>
-      <DESCRIPTION>This study aimed to allow for uploading sequences from PubSeq</DESCRIPTION>
+      <DESCRIPTION>This is a test to allow for uploading sequences from PubSeq</DESCRIPTION>
       <SUBMISSION_PROJECT>
          <SEQUENCING_PROJECT/>
       </SUBMISSION_PROJECT>
diff --git a/scripts/submit_ebi/example/sample-submission.xml b/scripts/submit_ebi/example/sample-submission.xml
new file mode 100644
index 0000000..9d13512
--- /dev/null
+++ b/scripts/submit_ebi/example/sample-submission.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<SUBMISSION>
+   <ACTIONS>
+      <ACTION>
+         <ADD/>
+      </ACTION>
+   </ACTIONS>
+</SUBMISSION>
diff --git a/scripts/submit_ebi/example/sample.xml b/scripts/submit_ebi/example/sample.xml
new file mode 100644
index 0000000..694c471
--- /dev/null
+++ b/scripts/submit_ebi/example/sample.xml
@@ -0,0 +1,68 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<SAMPLE_SET>
+  <SAMPLE alias="PubSeqSam0001" center_name="PubSeq01">
+    <TITLE>human gastric microbiota, mucosal</TITLE>
+    <SAMPLE_NAME>
+      <TAXON_ID>1284369</TAXON_ID>
+      <SCIENTIFIC_NAME>stomach metagenome</SCIENTIFIC_NAME>
+      <COMMON_NAME></COMMON_NAME>
+    </SAMPLE_NAME>
+    <SAMPLE_ATTRIBUTES>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>investigation type</TAG>
+        <VALUE>mimarks-survey</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>sequencing method</TAG>
+        <VALUE>pyrosequencing</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>collection date</TAG>
+        <VALUE>2010</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>host body site</TAG>
+        <VALUE>Mucosa of stomach</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>human-associated environmental package</TAG>
+        <VALUE>human-associated</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>geographic location (latitude)</TAG>
+        <VALUE>1.81</VALUE>
+     <UNITS>DD</UNITS>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>geographic location (longitude)</TAG>
+        <VALUE>-78.76</VALUE>
+     <UNITS>DD</UNITS>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+     <TAG>geographic location (country and/or sea)</TAG>
+     <VALUE>Colombia</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>geographic location (region and locality)</TAG>
+        <VALUE>Tumaco</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>environment (biome)</TAG>
+        <VALUE>coast</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>environment (feature)</TAG>
+        <VALUE>human-associated habitat</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>environment (material)</TAG>
+        <VALUE>gastric biopsy</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>ENA-CHECKLIST</TAG>
+        <VALUE>ERC000011</VALUE>
+      </SAMPLE_ATTRIBUTE>
+    </SAMPLE_ATTRIBUTES>
+  </SAMPLE>
+</SAMPLE_SET>
+
author	Pjotr Prins	2020-07-17 12:05:53 +0100
committer	Pjotr Prins	2020-07-17 12:08:43 +0100
commit	6ade3c1d47a83f0ed52a4efe287017b6a0fcc44e (patch)
tree	00f28ae6d9e973098aaee08534aa8414d54a957b
parent	4f3469e2d5395526c0376688ded4340a4834677d (diff)
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