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diff --git a/doc/blog/using-covid-19-pubseq-part1.html b/doc/blog/using-covid-19-pubseq-part1.html index 1959fac..0e6136c 100644 --- a/doc/blog/using-covid-19-pubseq-part1.html +++ b/doc/blog/using-covid-19-pubseq-part1.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> -<!-- 2020-05-29 Fri 12:06 --> +<!-- 2020-07-17 Fri 05:05 --> <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 1)</title> @@ -248,20 +248,20 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org9afe6ab">1. What does this mean?</a></li> -<li><a href="#orgf4bc3d4">2. Fetch sequence data</a></li> -<li><a href="#org9d7d482">3. Predicates</a></li> -<li><a href="#orgc6046bb">4. Fetch submitter info and other metadata</a></li> -<li><a href="#orgdcb216b">5. Fetch all sequences from Washington state</a></li> -<li><a href="#org7060f51">6. Discussion</a></li> -<li><a href="#orgdc51ccc">7. Acknowledgements</a></li> +<li><a href="#org0db5db0">1. What does this mean?</a></li> +<li><a href="#orge5267fd">2. Fetch sequence data</a></li> +<li><a href="#orgfbd3adc">3. Predicates</a></li> +<li><a href="#org08e70e1">4. Fetch submitter info and other metadata</a></li> +<li><a href="#org9194557">5. Fetch all sequences from Washington state</a></li> +<li><a href="#org76317ad">6. Discussion</a></li> +<li><a href="#orgeb871a1">7. Acknowledgements</a></li> </ul> </div> </div> -<div id="outline-container-org9afe6ab" class="outline-2"> -<h2 id="org9afe6ab"><span class="section-number-2">1</span> What does this mean?</h2> +<div id="outline-container-org0db5db0" class="outline-2"> +<h2 id="org0db5db0"><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 @@ -274,24 +274,24 @@ expressed in a <a href="https://github.com/arvados/bh20-seq-resource/blob/master 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 + doc: Host species as defined in NCBITaxon, e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 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> + _id: http://www.ebi.ac.uk/efo/EFO_0000532 + _type: "@id" + noLinkCheck: true 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> + doc: Sex of the host as defined in PATO, expect male () or female () 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> + _id: http://purl.obolibrary.org/obo/PATO_0000047 + _type: "@id" + noLinkCheck: true 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> + doc: Age of the host as number (e.g. 50) type: int? jsonldPredicate: - _id: http://purl.obolibrary.org/obo/PATO_<span style="color: #8bc34a;">0000011</span> + _id: http://purl.obolibrary.org/obo/PATO_0000011 </pre> </div> @@ -314,8 +314,8 @@ initiative! </div> -<div id="outline-container-orgf4bc3d4" class="outline-2"> -<h2 id="orgf4bc3d4"><span class="section-number-2">2</span> Fetch sequence data</h2> +<div id="outline-container-orge5267fd" class="outline-2"> +<h2 id="orge5267fd"><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 @@ -339,8 +339,8 @@ these identifiers throughout. </div> </div> -<div id="outline-container-org9d7d482" class="outline-2"> -<h2 id="org9d7d482"><span class="section-number-2">3</span> Predicates</h2> +<div id="outline-container-orgfbd3adc" class="outline-2"> +<h2 id="orgfbd3adc"><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 @@ -350,10 +350,10 @@ the following in a SPARQL end point </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> +<pre class="src src-sql">select distinct ?p +{ ?o ?p ?s -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -364,10 +364,10 @@ To get a <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&q </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 class="src src-sql">select distinct ?g +{ + GRAPH ?g {?s ?p ?o} +} </pre> </div> @@ -383,10 +383,10 @@ 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 class="src src-sql">select distinct ?s +{ + ?o <http://biohackathon.org/bh20-seq-schema#MainSchema/submitter> ?s +} </pre> </div> @@ -397,11 +397,11 @@ 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 . +<pre class="src src-sql">select distinct ?s +{ + ?o <http://biohackathon.org/bh20-seq-schema#MainSchema/submitter> ?id . ?id ?p ?s -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -415,12 +415,12 @@ 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> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?dataset ?submitter +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -438,32 +438,32 @@ Now we got this far, lets <a href="http://sparql.genenetwork.org/sparql/?default </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> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select (COUNT(distinct ?dataset) as ?num) +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter -<span style="color: #e91e63;">}</span> +} </pre> </div> </div> </div> -<div id="outline-container-orgc6046bb" class="outline-2"> -<h2 id="orgc6046bb"><span class="section-number-2">4</span> Fetch submitter info and other metadata</h2> +<div id="outline-container-org08e70e1" class="outline-2"> +<h2 id="org08e70e1"><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> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?dataset ?p ?submitter +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -480,13 +480,13 @@ 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> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?dataset ?submitter +{ ?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> + FILTER(CONTAINS(?submitter,"Roychoudhury")) . +} </pre> </div> @@ -496,12 +496,12 @@ 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> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?p +{ ?dataset ?p ?o . ?dataset pubseq:submitter ?id . -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -513,15 +513,15 @@ Let's zoom in on those of Roychoudhury with <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> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?sid ?sample ?p1 ?dataset ?submitter +{ ?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> . + FILTER(CONTAINS(?submitter,"Roychoudhury")) . ?dataset pubseq:sample ?sid . ?sid ?p1 ?sample -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -532,18 +532,13 @@ this database. Let's focus on one sample "MT326090.1" with predicate </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> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +PREFIX sio: <http://semanticscience.org/resource/> +select distinct ?sample ?p ?o +{ ?sample sio:SIO_000115 "MT326090.1" . ?sample ?p ?o . -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -561,8 +556,8 @@ to view/query the database. </div> </div> -<div id="outline-container-orgdcb216b" class="outline-2"> -<h2 id="orgdcb216b"><span class="section-number-2">5</span> Fetch all sequences from Washington state</h2> +<div id="outline-container-org9194557" class="outline-2"> +<h2 id="org9194557"><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 @@ -570,15 +565,11 @@ 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 class="src src-sql">select ?seq ?sample +{ + ?seq <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223> +} </pre> </div> @@ -586,11 +577,26 @@ and fetch all sequences referring to Washington state which lists 300 sequences originating from Washington state! Which is almost half of the set coming out of GenBank. </p> + +<p> +Likewise to list all sequences from Turkey we can find the wikidata +entity is <a href="https://www.wikidata.org/wiki/Q43">Q43</a>: +</p> + +<div class="org-src-container"> +<pre class="src src-sql">select ?seq ?sample +{ + ?seq <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q43> +} +</pre> </div> </div> +</div> + -<div id="outline-container-org7060f51" class="outline-2"> -<h2 id="org7060f51"><span class="section-number-2">6</span> Discussion</h2> +<div id="outline-container-org76317ad" class="outline-2"> +<h2 id="org76317ad"><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 @@ -601,8 +607,8 @@ referenced in publications and origins are citeable. </div> </div> -<div id="outline-container-orgdc51ccc" class="outline-2"> -<h2 id="orgdc51ccc"><span class="section-number-2">7</span> Acknowledgements</h2> +<div id="outline-container-orgeb871a1" class="outline-2"> +<h2 id="orgeb871a1"><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 @@ -617,7 +623,7 @@ Garrison this initiative would not have existed! </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 12:06</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 2020-07-17 Fri 05:02</small>. </div> </body> </html> |