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<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=&query=select+distinct+%3Fg%0D%0A%7B%0D%0A++++GRAPH+%3Fg+%7B%3Fs+%3Fp+%3Fo%7D%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&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&query=select+distinct+%3Fp%0D%0A%7B%0D%0A+++%3Fo+%3Fp+%3Fs%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&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"><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></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"><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></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/"><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/></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=&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&format=text%2Fhtml&timeout=0&debug=on&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&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+&format=text%2Fhtml&timeout=0&debug=on&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/"><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/></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/"><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/></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/"><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/></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/"><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/></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/"><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/></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=&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&format=text%2Fhtml&timeout=0&debug=on&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/>
PREFIX sio: <http://semanticscience.org/resource/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/>
PREFIX sio: <http://semanticscience.org/resource/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/>
PREFIX sio: <http://semanticscience.org/resource/">#MainSchema/>
</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/>
PREFIX sio: <http://semanticscience.org/resource/">PREFIX</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/>
PREFIX sio: <http://semanticscience.org/resource/"> sio: <http://semanticscience.org/resource/></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=&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&format=text%2Fhtml&timeout=0&debug=on&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> ?sample .
?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample .
?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample .
?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223">#MainSchema/sample> ?sample .
?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223></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>
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