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<div id="content">
<h1 class="title">COVID-19 PubSeq (part 4)</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org871ad58">1. Modify Metadata</a></li>
<li><a href="#org07e8755">2. What is the schema?</a></li>
<li><a href="#org4857280">3. How is the website generated?</a></li>
<li><a href="#orge709ae2">4. Modifying the schema</a></li>
</ul>
</div>
</div>
<div id="outline-container-org871ad58" class="outline-2">
<h2 id="org871ad58"><span class="section-number-2">1</span> Modify Metadata</h2>
<div class="outline-text-2" id="text-1">
<p>
The public sequence resource uses multiple data formats listed on the
<a href="./download">DOWNLOAD</a> page. One of the most exciting features is the full support
for RDF and semantic web/linked data ontologies. This technology
allows for querying data in unprescribed ways - that is, you can
formulate your own queries without dealing with a preset model of that
data (so typical of CSV files and SQL tables). Examples of exploring
data are listed <a href="./blog?id=using-covid-19-pubseq-part1">here</a>.
</p>
<p>
In this BLOG we are going to look at the metadata entered on the
<a href="./">COVID-19 PubSeq</a> website (or command line client). It is important to
understand that anyone, including you, can change that information!
</p>
</div>
</div>
<div id="outline-container-org07e8755" class="outline-2">
<h2 id="org07e8755"><span class="section-number-2">2</span> What is the schema?</h2>
<div class="outline-text-2" id="text-2">
<p>
The default metadata schema is listed <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml">here</a>.
</p>
</div>
</div>
<div id="outline-container-org4857280" class="outline-2">
<h2 id="org4857280"><span class="section-number-2">3</span> How is the website generated?</h2>
<div class="outline-text-2" id="text-3">
<p>
Using the schema we use <a href="https://pypi.org/project/PyShEx/">pyshex</a> shex expressions and <a href="https://github.com/common-workflow-language/schema_salad">schema salad</a> to
generate the <a href="https://github.com/arvados/bh20-seq-resource/blob/edb17e7f7caebfa1e76b21006b1772a33f4f7887/bh20simplewebuploader/templates/form.html#L47">input form</a>, <a href="https://github.com/arvados/bh20-seq-resource/blob/edb17e7f7caebfa1e76b21006b1772a33f4f7887/bh20sequploader/qc_metadata.py#L13">validate</a> the user input and to build <a href="https://github.com/arvados/bh20-seq-resource/blob/edb17e7f7caebfa1e76b21006b1772a33f4f7887/workflows/pangenome-generate/merge-metadata.py#L24">RDF</a>!
All from that one metadata schema.
</p>
</div>
</div>
<div id="outline-container-orge709ae2" class="outline-2">
<h2 id="orge709ae2"><span class="section-number-2">4</span> Modifying the schema</h2>
<div class="outline-text-2" id="text-4">
<p>
One of the first things we wanted to do is to add a field for the data
license. Initially we only support CC-4.0 as a license by default, but
now we want to give uploaders the option to make it an even more
liberal CC0 license. The first step is to find a good ontology term
for the field. Searching for `creative commons cc0 rdf' rendered this
useful <a href="https://creativecommons.org/ns">page</a>. We also find an <a href="https://wiki.creativecommons.org/wiki/CC_License_Rdf_Overview">overview</a> where CC0 is represented as URI
<a href="https://creativecommons.org/publicdomain/zero/1.0/">https://creativecommons.org/publicdomain/zero/1.0/</a>. Meanwhile the
attribution license <a href="https://creativecommons.org/licenses/by/4.0/">https://creativecommons.org/licenses/by/4.0/</a>.
According to this <a href="https://wiki.creativecommons.org/images/d/d6/Ccrel-1.0.pdf">document</a> we should really also add fields for
attributionName and attributionURL.
</p>
<p>
<i>Note: work in progress</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 2020-07-12 Sun 06:24</small>.
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