aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--bh20simplewebuploader/templates/blog.html8
-rw-r--r--doc/blog/using-covid-19-pubseq-part6.html393
-rw-r--r--doc/blog/using-covid-19-pubseq-part6.org7
-rw-r--r--scripts/submit_ebi/example/project-submission.xml3
-rw-r--r--scripts/submit_ebi/example/project.xml3
-rw-r--r--scripts/submit_ebi/example/sample-submission.xml8
-rw-r--r--scripts/submit_ebi/example/sample.xml68
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 @@
+<?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; }
+ .done { font-family: monospace; color: green; }
+ .priority { font-family: monospace; color: orange; }
+ .tag { background-color: #eee; font-family: monospace;
+ padding: 2px; font-size: 80%; font-weight: normal; }
+ .timestamp { color: #bebebe; }
+ .timestamp-kwd { color: #5f9ea0; }
+ .org-right { margin-left: auto; margin-right: 0px; text-align: right; }
+ .org-left { margin-left: 0px; margin-right: auto; text-align: left; }
+ .org-center { margin-left: auto; margin-right: auto; text-align: center; }
+ .underline { text-decoration: underline; }
+ #postamble p, #preamble p { font-size: 90%; margin: .2em; }
+ p.verse { margin-left: 3%; }
+ pre {
+ border: 1px solid #ccc;
+ box-shadow: 3px 3px 3px #eee;
+ padding: 8pt;
+ font-family: monospace;
+ overflow: auto;
+ margin: 1.2em;
+ }
+ pre.src {
+ position: relative;
+ overflow: visible;
+ padding-top: 1.2em;
+ }
+ pre.src:before {
+ display: none;
+ position: absolute;
+ background-color: white;
+ top: -10px;
+ right: 10px;
+ padding: 3px;
+ border: 1px solid black;
+ }
+ pre.src:hover:before { display: inline;}
+ /* Languages per Org manual */
+ pre.src-asymptote:before { content: 'Asymptote'; }
+ pre.src-awk:before { content: 'Awk'; }
+ pre.src-C:before { content: 'C'; }
+ /* pre.src-C++ doesn't work in CSS */
+ pre.src-clojure:before { content: 'Clojure'; }
+ pre.src-css:before { content: 'CSS'; }
+ pre.src-D:before { content: 'D'; }
+ pre.src-ditaa:before { content: 'ditaa'; }
+ pre.src-dot:before { content: 'Graphviz'; }
+ pre.src-calc:before { content: 'Emacs Calc'; }
+ pre.src-emacs-lisp:before { content: 'Emacs Lisp'; }
+ pre.src-fortran:before { content: 'Fortran'; }
+ pre.src-gnuplot:before { content: 'gnuplot'; }
+ pre.src-haskell:before { content: 'Haskell'; }
+ pre.src-hledger:before { content: 'hledger'; }
+ pre.src-java:before { content: 'Java'; }
+ pre.src-js:before { content: 'Javascript'; }
+ pre.src-latex:before { content: 'LaTeX'; }
+ pre.src-ledger:before { content: 'Ledger'; }
+ pre.src-lisp:before { content: 'Lisp'; }
+ pre.src-lilypond:before { content: 'Lilypond'; }
+ pre.src-lua:before { content: 'Lua'; }
+ pre.src-matlab:before { content: 'MATLAB'; }
+ pre.src-mscgen:before { content: 'Mscgen'; }
+ pre.src-ocaml:before { content: 'Objective Caml'; }
+ pre.src-octave:before { content: 'Octave'; }
+ pre.src-org:before { content: 'Org mode'; }
+ pre.src-oz:before { content: 'OZ'; }
+ pre.src-plantuml:before { content: 'Plantuml'; }
+ pre.src-processing:before { content: 'Processing.js'; }
+ pre.src-python:before { content: 'Python'; }
+ pre.src-R:before { content: 'R'; }
+ pre.src-ruby:before { content: 'Ruby'; }
+ pre.src-sass:before { content: 'Sass'; }
+ pre.src-scheme:before { content: 'Scheme'; }
+ pre.src-screen:before { content: 'Gnu Screen'; }
+ pre.src-sed:before { content: 'Sed'; }
+ pre.src-sh:before { content: 'shell'; }
+ pre.src-sql:before { content: 'SQL'; }
+ pre.src-sqlite:before { content: 'SQLite'; }
+ /* additional languages in org.el's org-babel-load-languages alist */
+ pre.src-forth:before { content: 'Forth'; }
+ pre.src-io:before { content: 'IO'; }
+ pre.src-J:before { content: 'J'; }
+ pre.src-makefile:before { content: 'Makefile'; }
+ pre.src-maxima:before { content: 'Maxima'; }
+ pre.src-perl:before { content: 'Perl'; }
+ pre.src-picolisp:before { content: 'Pico Lisp'; }
+ pre.src-scala:before { content: 'Scala'; }
+ pre.src-shell:before { content: 'Shell Script'; }
+ pre.src-ebnf2ps:before { content: 'ebfn2ps'; }
+ /* additional language identifiers per "defun org-babel-execute"
+ in ob-*.el */
+ pre.src-cpp:before { content: 'C++'; }
+ pre.src-abc:before { content: 'ABC'; }
+ pre.src-coq:before { content: 'Coq'; }
+ pre.src-groovy:before { content: 'Groovy'; }
+ /* additional language identifiers from org-babel-shell-names in
+ ob-shell.el: ob-shell is the only babel language using a lambda to put
+ the execution function name together. */
+ pre.src-bash:before { content: 'bash'; }
+ pre.src-csh:before { content: 'csh'; }
+ pre.src-ash:before { content: 'ash'; }
+ pre.src-dash:before { content: 'dash'; }
+ pre.src-ksh:before { content: 'ksh'; }
+ pre.src-mksh:before { content: 'mksh'; }
+ pre.src-posh:before { content: 'posh'; }
+ /* Additional Emacs modes also supported by the LaTeX listings package */
+ pre.src-ada:before { content: 'Ada'; }
+ pre.src-asm:before { content: 'Assembler'; }
+ pre.src-caml:before { content: 'Caml'; }
+ pre.src-delphi:before { content: 'Delphi'; }
+ pre.src-html:before { content: 'HTML'; }
+ pre.src-idl:before { content: 'IDL'; }
+ pre.src-mercury:before { content: 'Mercury'; }
+ pre.src-metapost:before { content: 'MetaPost'; }
+ pre.src-modula-2:before { content: 'Modula-2'; }
+ pre.src-pascal:before { content: 'Pascal'; }
+ pre.src-ps:before { content: 'PostScript'; }
+ pre.src-prolog:before { content: 'Prolog'; }
+ pre.src-simula:before { content: 'Simula'; }
+ pre.src-tcl:before { content: 'tcl'; }
+ pre.src-tex:before { content: 'TeX'; }
+ pre.src-plain-tex:before { content: 'Plain TeX'; }
+ pre.src-verilog:before { content: 'Verilog'; }
+ pre.src-vhdl:before { content: 'VHDL'; }
+ pre.src-xml:before { content: 'XML'; }
+ pre.src-nxml:before { content: 'XML'; }
+ /* add a generic configuration mode; LaTeX export needs an additional
+ (add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */
+ pre.src-conf:before { content: 'Configuration File'; }
+
+ table { border-collapse:collapse; }
+ caption.t-above { caption-side: top; }
+ caption.t-bottom { caption-side: bottom; }
+ td, th { vertical-align:top; }
+ th.org-right { text-align: center; }
+ th.org-left { text-align: center; }
+ th.org-center { text-align: center; }
+ td.org-right { text-align: right; }
+ td.org-left { text-align: left; }
+ td.org-center { text-align: center; }
+ dt { font-weight: bold; }
+ .footpara { display: inline; }
+ .footdef { margin-bottom: 1em; }
+ .figure { padding: 1em; }
+ .figure p { text-align: center; }
+ .equation-container {
+ display: table;
+ text-align: center;
+ width: 100%;
+ }
+ .equation {
+ vertical-align: middle;
+ }
+ .equation-label {
+ display: table-cell;
+ 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">&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>
+