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authorPjotr Prins2020-05-29 11:00:08 -0500
committerPjotr Prins2020-05-29 11:00:08 -0500
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parent50a9933a997e468db3343023a580308b28edc653 (diff)
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+<title>COVID-19 PubSeq (part 1)</title>
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+<link rel="Blog stylesheet" type="text/css" href="blog.css" />
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+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
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+through which recipients can access the Corresponding Source.
+
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+ }
+/*]]>*///-->
+</script>
+</head>
+<body>
+<div id="org-div-home-and-up">
+ <a accesskey="h" href=""> UP </a>
+ |
+ <a accesskey="H" href="http://covid19.genenetwork.org"> HOME </a>
+</div><div id="content">
+<h1 class="title">COVID-19 PubSeq (part 1)</h1>
+<div id="table-of-contents">
+<h2>Table of Contents</h2>
+<div id="text-table-of-contents">
+<ul>
+<li><a href="#org5e85b09">1. What does this mean?</a></li>
+<li><a href="#org038e367">2. Fetch sequence data</a></li>
+<li><a href="#org3ad046c">3. Predicates</a></li>
+<li><a href="#orga4e7054">4. Fetch submitter info and other metadata</a></li>
+<li><a href="#orgc50badd">5. Fetch all sequences from Washington state</a></li>
+<li><a href="#orgbc80874">6. Discussion</a></li>
+<li><a href="#orgce8eaf6">7. Acknowledgements</a></li>
+</ul>
+</div>
+</div>
+<p>
+As part of the COVID-19 Biohackathon 2020 we formed a working group
+to create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
+Corona virus sequences. The general idea is to create a repository
+that has a low barrier to entry for uploading sequence data using best
+practices. I.e., data published with a creative commons 4.0 (CC-4.0)
+license with metadata using state-of-the art standards and, perhaps
+most importantly, providing standardised workflows that get triggered
+on upload, so that results are immediately available in standardised
+data formats.
+</p>
+
+<div id="outline-container-org5e85b09" class="outline-2">
+<h2 id="org5e85b09"><span class="section-number-2">1</span> What does this mean?</h2>
+<div class="outline-text-2" id="text-1">
+<p>
+This means that when someone uploads a SARS-CoV-2 sequence using one
+of our tools (CLI or web-based) they add some metadata which is
+expressed in a <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml">schema</a> that looks like
+</p>
+
+<div class="org-src-container">
+<pre class="src src-json">- name: hostSchema
+ type: record
+ fields:
+ host_species:
+ doc: Host species as defined in NCBITaxon, e.g. http://purl.obolibrary.org/obo/NCBITaxon_<span style="color: #8bc34a;">9606</span> for Homo sapiens
+ type: string
+ jsonldPredicate:
+ _id: http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0000532</span>
+ _type: <span style="color: #9ccc65;">"@id"</span>
+ noLinkCheck: <span style="color: #8bc34a;">true</span>
+ host_sex:
+ doc: Sex of the host as defined in PATO, expect male <span style="color: #e91e63;">()</span> or female <span style="color: #e91e63;">()</span>
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/PATO_<span style="color: #8bc34a;">0000047</span>
+ _type: <span style="color: #9ccc65;">"@id"</span>
+ noLinkCheck: <span style="color: #8bc34a;">true</span>
+ host_age:
+ doc: Age of the host as number <span style="color: #e91e63;">(</span>e.g. <span style="color: #8bc34a;">50</span><span style="color: #e91e63;">)</span>
+ type: int?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/PATO_<span style="color: #8bc34a;">0000011</span>
+</pre>
+</div>
+
+<p>
+this metadata gets transformed into an RDF database which means
+information can easily be fetched related to uploaded sequences.
+We'll show an example below where we query a live database.
+</p>
+
+<p>
+There is more: when a new sequence gets uploaded COVID-19 PubSeq kicks
+in with a number of workflows running in the cloud. These workflows
+generate a fresh variation graph (GFA) containing all sequences, an
+RDF file containing metadata, and an RDF file containing the variation
+graph in triples. Soon we will at multi sequence alignments (MSA) and
+more. Anyone can contribute data, tools and workflows to this
+initiative!
+</p>
+</div>
+</div>
+
+
+<div id="outline-container-org038e367" class="outline-2">
+<h2 id="org038e367"><span class="section-number-2">2</span> Fetch sequence data</h2>
+<div class="outline-text-2" id="text-2">
+<p>
+The latest run of the pipeline can be viewed <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">here</a>. Each of these
+generated files can just be downloaded for your own use and sharing!
+Data is published under a <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons 4.0 attribution license</a>
+(CC-BY-4.0). This means that, unlike some other 'public' resources,
+you can use this data in any way you want, provided the submitter gets
+attributed.
+</p>
+
+<p>
+If you download the GFA or FASTA sequences you'll find sequences are
+named something like
+<b>keep:e17abc8a0269875ed4cfbff5d9897c6c+123/sequence.fasta</b> which
+refers to an internal Arvados Keep representation of the FASTA
+sequence. Keep is content-addressable which means that the value
+e17abc8a0269875ed4cfbff5d9897c6c uniquely identifies the file by its
+contents. If the contents change, the identifier changes! We use
+these identifiers throughout.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org3ad046c" class="outline-2">
+<h2 id="org3ad046c"><span class="section-number-2">3</span> Predicates</h2>
+<div class="outline-text-2" id="text-3">
+<p>
+To explore an RDF dataset, the first query we can do is open and gets
+us a list. Lets look at all the predicates in the dataset by pasting
+the following in a SPARQL end point
+<a href="http://sparql.genenetwork.org/sparql/">http://sparql.genenetwork.org/sparql/</a>
+</p>
+
+<div class="org-src-container">
+<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?p
+<span style="color: #e91e63;">{</span>
+ ?o ?p ?s
+<span style="color: #e91e63;">}</span>
+</pre>
+</div>
+
+<p>
+you can ignore the openlink and w3 ones. To reduce results to a named
+graph set the default graph.
+To get a <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;query=select+distinct+%3Fg%0D%0A%7B%0D%0A++++GRAPH+%3Fg+%7B%3Fs+%3Fp+%3Fo%7D%0D%0A%7D&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">list of graphs</a> in the dataset, first do
+</p>
+
+<div class="org-src-container">
+<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?g
+<span style="color: #e91e63;">{</span>
+ GRAPH ?g <span style="color: #2196F3;">{</span>?s ?p ?o<span style="color: #2196F3;">}</span>
+<span style="color: #e91e63;">}</span>
+</pre>
+</div>
+
+<p>
+Limiting search to metadata add
+<a href="http://covid-19.genenetwork.org/graph/metadata.ttl">http://covid-19.genenetwork.org/graph/metadata.ttl</a> in the top input
+box. Now you can find a <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=http%3A%2F%2Fcovid-19.genenetwork.org%2Fgraph%2Fmetadata.ttl&amp;query=select+distinct+%3Fp%0D%0A%7B%0D%0A+++%3Fo+%3Fp+%3Fs%0D%0A%7D&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">predicate</a> for submitter that looks like
+<a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">http://biohackathon.org/bh20-seq-schema#MainSchema/submitter</a>.
+</p>
+
+<p>
+To list all submitters, try
+</p>
+
+<div class="org-src-container">
+<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?s
+<span style="color: #e91e63;">{</span>
+ ?o <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">#MainSchema/submitter&gt;</a> ?s
+<span style="color: #e91e63;">}</span>
+</pre>
+</div>
+
+<p>
+Oh wait, it returns things like nodeID://b76150! That is not helpful,
+these are anonymous nodes in the graph. These point to another triple
+and by
+</p>
+
+<div class="org-src-container">
+<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?s
+<span style="color: #e91e63;">{</span>
+ ?o <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">#MainSchema/submitter&gt;</a> ?id .
+ ?id ?p ?s
+<span style="color: #e91e63;">}</span>
+</pre>
+</div>
+
+<p>
+you get a list of all submitters including "University of Washington,
+Seattle, WA 98109, USA".
+</p>
+
+<p>
+To lift the full URL out of the query you can use a header like
+</p>
+
+<div class="org-src-container">
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?submitter
+<span style="color: #e91e63;">{</span>
+ ?dataset pubseq:submitter ?id .
+ ?id ?p ?submitter
+<span style="color: #e91e63;">}</span>
+</pre>
+</div>
+
+<p>
+which reads a bit better. We can also see the <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0Aselect+distinct+%3Fdataset+%3Fsubmitter%0D%0A%7B%0D%0A+++%3Fdataset+pubseq%3Asubmitter+%3Fid+.%0D%0A+++%3Fid+%3Fp+%3Fsubmitter%0D%0A%7D%0D%0A&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">submitted sequences</a>. One
+of them submitted by University of Washington is
+<a href="http://collections.lugli.arvadosapi.com/c=030bcb8fda7f19743157359f5855f7a6+126/sequence.fasta">http://collections.lugli.arvadosapi.com/c=030bcb8fda7f19743157359f5855f7a6+126/sequence.fasta</a>
+(note the ID may have changed so pick one with above query).
+To see the submitted metadata replace sequence.fasta with metadata.yaml
+<a href="http://collections.lugli.arvadosapi.com/c=030bcb8fda7f19743157359f5855f7a6+126/metadata.yaml">http://collections.lugli.arvadosapi.com/c=030bcb8fda7f19743157359f5855f7a6+126/metadata.yaml</a>
+</p>
+
+<p>
+Now we got this far, lets <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=http%3A%2F%2Fcovid-19.genenetwork.org%2Fgraph%2Fmetadata.ttl&amp;query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0Aselect+%28COUNT%28distinct+%3Fdataset%29+as+%3Fnum%29%0D%0A%7B%0D%0A+++%3Fdataset+pubseq%3Asubmitter+%3Fid+.%0D%0A+++%3Fid+%3Fp+%3Fsubmitter%0D%0A%7D+&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">count the datasets</a> submitted with
+</p>
+
+<div class="org-src-container">
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #e91e63;">(</span><span style="color: #ff8A65;">COUNT</span><span style="color: #2196F3;">(</span><span style="color: #fff59d;">distinct</span> ?dataset<span style="color: #2196F3;">)</span> <span style="color: #fff59d;">as</span> ?num<span style="color: #e91e63;">)</span>
+<span style="color: #e91e63;">{</span>
+ ?dataset pubseq:submitter ?id .
+ ?id ?p ?submitter
+<span style="color: #e91e63;">}</span>
+</pre>
+</div>
+</div>
+</div>
+
+
+<div id="outline-container-orga4e7054" class="outline-2">
+<h2 id="orga4e7054"><span class="section-number-2">4</span> Fetch submitter info and other metadata</h2>
+<div class="outline-text-2" id="text-4">
+<p>
+To get dataests with submitters we can do the above
+</p>
+
+<div class="org-src-container">
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?p ?submitter
+<span style="color: #e91e63;">{</span>
+ ?dataset pubseq:submitter ?id .
+ ?id ?p ?submitter
+<span style="color: #e91e63;">}</span>
+</pre>
+</div>
+
+<p>
+Tells you one submitter is "Roychoudhury,P.;Greninger,A.;Jerome,K."
+with a URL <a href="http://purl.obolibrary.org/obo/NCIT_C42781">predicate</a> (<a href="http://purl.obolibrary.org/obo/NCIT_C42781">http://purl.obolibrary.org/obo/NCIT_C42781</a>)
+explaining "The individual who is responsible for the content of a
+document." Well formed URIs point to real information about the URI
+itself. Welcome to the power of the semantic web.
+</p>
+
+<p>
+Let's focus on one sample with
+</p>
+
+<div class="org-src-container">
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?submitter
+<span style="color: #e91e63;">{</span>
+ ?dataset pubseq:submitter ?id .
+ ?id ?p ?submitter .
+ FILTER<span style="color: #2196F3;">(</span><span style="color: #fff59d;">CONTAINS</span><span style="color: #EF6C00;">(</span>?submitter,"Roychoudhury"<span style="color: #EF6C00;">)</span><span style="color: #2196F3;">)</span> .
+<span style="color: #e91e63;">}</span>
+</pre>
+</div>
+
+<p>
+That is a lot of samples! We just want to pick one, so let's
+see if we can get a sample ID by listing sample predicates
+</p>
+
+<div class="org-src-container">
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?p
+<span style="color: #e91e63;">{</span>
+ ?dataset ?p ?o .
+ ?dataset pubseq:submitter ?id .
+<span style="color: #e91e63;">}</span>
+</pre>
+</div>
+
+<p>
+which lists a predicate named
+<a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample">http://biohackathon.org/bh20-seq-schema#MainSchema/sample</a>.
+Let's zoom in on those of Roychoudhury with
+</p>
+
+
+<div class="org-src-container">
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?sid ?sample ?p1 ?dataset ?submitter
+<span style="color: #e91e63;">{</span>
+ ?dataset pubseq:submitter ?id .
+ ?id ?p ?submitter .
+ FILTER<span style="color: #2196F3;">(</span><span style="color: #fff59d;">CONTAINS</span><span style="color: #EF6C00;">(</span>?submitter,"Roychoudhury"<span style="color: #EF6C00;">)</span><span style="color: #2196F3;">)</span> .
+ ?dataset pubseq:sample ?sid .
+ ?sid ?p1 ?sample
+<span style="color: #e91e63;">}</span>
+</pre>
+</div>
+
+<p>
+which shows pretty much <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0Aselect+distinct+%3Fsid+%3Fsample+%3Fp1+%3Fdataset+%3Fsubmitter%0D%0A%7B%0D%0A+++%3Fdataset+pubseq%3Asubmitter+%3Fid+.%0D%0A+++%3Fid+%3Fp+%3Fsubmitter+.%0D%0A+++FILTER%28CONTAINS%28%3Fsubmitter%2C%22Roychoudhury%22%29%29+.%0D%0A+++%3Fdataset+pubseq%3Asample+%3Fsid+.%0D%0A+++%3Fsid+%3Fp1+%3Fsample%0D%0A%7D&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">everything known</a> about their submissions in
+this database. Let's focus on one sample "MT326090.1" with predicate
+<a href="http://semanticscience.org/resource/SIO_000115">http://semanticscience.org/resource/SIO_000115</a>.
+</p>
+
+<div class="org-src-container">
+<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+PREFIX sio: &lt;http://semanticscience.org/resource/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+PREFIX sio: &lt;http://semanticscience.org/resource/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+PREFIX sio: &lt;http://semanticscience.org/resource/">#MainSchema/&gt;
+</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+PREFIX sio: &lt;http://semanticscience.org/resource/">PREFIX</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+PREFIX sio: &lt;http://semanticscience.org/resource/"> sio: &lt;http://semanticscience.org/resource/&gt;</a>
+<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?sample ?p ?o
+<span style="color: #e91e63;">{</span>
+ ?sample sio:SIO_000115 "MT326090.1" .
+ ?sample ?p ?o .
+<span style="color: #e91e63;">}</span>
+</pre>
+</div>
+
+<p>
+This <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0APREFIX+sio%3A+%3Chttp%3A%2F%2Fsemanticscience.org%2Fresource%2F%3E%0D%0Aselect+distinct+%3Fsample+%3Fp+%3Fo%0D%0A%7B%0D%0A+++%3Fsample+sio%3ASIO_000115+%22MT326090.1%22+.%0D%0A+++%3Fsample+%3Fp+%3Fo+.%0D%0A%7D&amp;format=text%2Fhtml&amp;timeout=0&amp;debug=on&amp;run=+Run+Query+">query</a> tells us the sample was submitted "2020-03-21" and
+originates from <a href="http://www.wikidata.org/entity/Q30">http://www.wikidata.org/entity/Q30</a>, i.e., the USA and
+is a biospecimen collected from the back of the throat by swabbing.
+We can track it back to the original GenBank <a href="http://identifiers.org/insdc/MT326090.1#sequence">submission</a>.
+</p>
+
+<p>
+We have also added country and label data to make it a bit easier
+to view/query the database.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgc50badd" class="outline-2">
+<h2 id="orgc50badd"><span class="section-number-2">5</span> Fetch all sequences from Washington state</h2>
+<div class="outline-text-2" id="text-5">
+<p>
+Now we know how to get at the origin we can do it the other way round
+and fetch all sequences referring to Washington state
+</p>
+
+<div class="org-src-container">
+<pre class="src src-sql">
+<span style="color: #fff59d;">select</span> ?seq ?sample
+<span style="color: #e91e63;">{</span>
+ ?seq <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223">#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223&gt;</a>
+<span style="color: #e91e63;">}</span>
+</pre>
+</div>
+
+<p>
+which lists 300 sequences originating from Washington state! Which is almost
+half of the set coming out of GenBank.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgbc80874" class="outline-2">
+<h2 id="orgbc80874"><span class="section-number-2">6</span> Discussion</h2>
+<div class="outline-text-2" id="text-6">
+<p>
+The public sequence uploader collects sequences, raw data and
+(machine) queriable metadata. Not only that: data gets analyzed in the
+pangenome and results are presented immediately. The data can be
+referenced in publications and origins are citeable.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgce8eaf6" class="outline-2">
+<h2 id="orgce8eaf6"><span class="section-number-2">7</span> Acknowledgements</h2>
+<div class="outline-text-2" id="text-7">
+<p>
+The overall effort was due to magnificent freely donated input by a
+great number of people. I particularly want to thank Thomas Liener for
+the great effort he made with the ontology group in getting ontology's
+and schema sorted! Peter Amstutz and <a href="https://arvados.org/">Arvados/Curii</a> helped build the
+on-demand compute and back-ends. Thanks also to Michael Crusoe for
+supporting the <a href="https://www.commonwl.org/">Common Workflow Language</a> initiative. And without Erik
+Garrison this initiative would not have existed!
+</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 2020-05-29 Fri 10:12</small>.
+</div>
+</body>
+</html>
diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html
index ac32717..7903791 100644
--- a/doc/blog/using-covid-19-pubseq-part3.html
+++ b/doc/blog/using-covid-19-pubseq-part3.html
@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
-<!-- 2020-05-27 Wed 07:41 -->
+<!-- 2020-05-29 Fri 10:00 -->
<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 Uploading Data (part 3)</title>
@@ -248,14 +248,16 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
-<li><a href="#org074cf76">1. Uploading Data</a></li>
-<li><a href="#org00e6dd5">2. What does this mean?</a></li>
+<li><a href="#orgbfd8594">1. Uploading Data</a></li>
+<li><a href="#org3243122">2. Introduction</a></li>
+<li><a href="#orgc7011c9">3. Step 1: Sequence</a></li>
+<li><a href="#org83d22ff">4. Step 2: Metadata</a></li>
</ul>
</div>
</div>
-<div id="outline-container-org074cf76" class="outline-2">
-<h2 id="org074cf76"><span class="section-number-2">1</span> Uploading Data</h2>
+<div id="outline-container-orgbfd8594" class="outline-2">
+<h2 id="orgbfd8594"><span class="section-number-2">1</span> Uploading Data</h2>
<div class="outline-text-2" id="text-1">
<p>
<i>Work in progress!</i>
@@ -263,12 +265,38 @@ for the JavaScript code in this tag.
</div>
</div>
-<div id="outline-container-org00e6dd5" class="outline-2">
-<h2 id="org00e6dd5"><span class="section-number-2">2</span> What does this mean?</h2>
+<div id="outline-container-org3243122" class="outline-2">
+<h2 id="org3243122"><span class="section-number-2">2</span> Introduction</h2>
+<div class="outline-text-2" id="text-2">
+<p>
+The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a
+public resource for global comparisons. Compute it triggered on
+upload. Read the <a href="./about">ABOUT</a> page for more information.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgc7011c9" class="outline-2">
+<h2 id="orgc7011c9"><span class="section-number-2">3</span> Step 1: Sequence</h2>
+<div class="outline-text-2" id="text-3">
+<p>
+We start with an assembled or mapped sequence in FASTA format. The
+PubSeq uploader contains a <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/qc_fasta.py">QC step</a> which checks whether it is a likely
+SARS-CoV-2 sequence. While PubSeq deduplicates sequences and never
+overwrites metadata it probably pays to check whether your data
+already is in the system by querying some metadata as described in
+<a href="./blog?id=using-covid-19-pubseq-part1">Query metadata with SPARQL</a>.
+</p>
+</div>
+</div>
+
+
+<div id="outline-container-org83d22ff" class="outline-2">
+<h2 id="org83d22ff"><span class="section-number-2">4</span> Step 2: Metadata</h2>
</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 2020-05-27 Wed 07:41</small>.
+<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 2020-05-29 Fri 10:00</small>.
</div>
</body>
</html>
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org
index 1cd2db1..296bef6 100644
--- a/doc/blog/using-covid-19-pubseq-part3.org
+++ b/doc/blog/using-covid-19-pubseq-part3.org
@@ -13,10 +13,24 @@
* Table of Contents :TOC:noexport:
- [[#uploading-data][Uploading Data]]
- - [[#table-of-contents][Table of Contents]]
- - [[#what-does-this-mean][What does this mean?]]
+ - [[#introduction][Introduction]]
+ - [[#step-1-sequence][Step 1: Sequence]]
+ - [[#step-2-metadata][Step 2: Metadata]]
+
+* Introduction
+
+The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a
+public resource for global comparisons. Compute it triggered on
+upload. Read the [[./about][ABOUT]] page for more information.
+
+* Step 1: Sequence
+
+We start with an assembled or mapped sequence in FASTA format. The
+PubSeq uploader contains a [[https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/qc_fasta.py][QC step]] which checks whether it is a likely
+SARS-CoV-2 sequence. While PubSeq deduplicates sequences and never
+overwrites metadata it probably pays to check whether your data
+already is in the system by querying some metadata as described in
+[[./blog?id=using-covid-19-pubseq-part1][Query metadata with SPARQL]].
-* Table of Contents :TOC:noexport:
- - [[#what-does-this-mean][What does this mean?]]
-* What does this mean?
+* Step 2: Metadata
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-22 01:25:40 +0000