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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 @@ +<?xml version="1.0" encoding="utf-8"?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" +"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> +<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" /> +<style type="text/css"> + <!--/*--><![CDATA[/*><!--*/ + .title { text-align: center; + margin-bottom: .2em; } + .subtitle { text-align: center; + font-size: medium; + font-weight: bold; + margin-top:0; } + .todo { font-family: monospace; color: red; 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+ text-align: right; + vertical-align: middle; + } + .inlinetask { + padding: 10px; + border: 2px solid gray; + margin: 10px; + background: #ffffcc; + } + #org-div-home-and-up + { text-align: right; font-size: 70%; white-space: nowrap; } + textarea { overflow-x: auto; } + .linenr { font-size: smaller } + .code-highlighted { background-color: #ffff00; } + .org-info-js_info-navigation { border-style: none; } + #org-info-js_console-label + { font-size: 10px; font-weight: bold; white-space: nowrap; } + .org-info-js_search-highlight + { background-color: #ffff00; color: #000000; font-weight: bold; } + .org-svg { width: 90%; } + /*]]>*/--> +</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. +*/ +<!--/*--><![CDATA[/*><!--*/ + function CodeHighlightOn(elem, id) + { + var target = document.getElementById(id); + if(null != target) { + elem.cacheClassElem = elem.className; + elem.cacheClassTarget = target.className; + target.className = "code-highlighted"; + elem.className = "code-highlighted"; + } + } + function CodeHighlightOff(elem, id) + { + var target = document.getElementById(id); + if(elem.cacheClassElem) + elem.className = elem.cacheClassElem; + if(elem.cacheClassTarget) + target.className = elem.cacheClassTarget; + } +/*]]>*///--> +</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"><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>. +</div> +</body> +</html> |