diff options
Diffstat (limited to 'doc/blog')
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part1.html | 257 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part1.org | 57 |
2 files changed, 224 insertions, 90 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part1.html b/doc/blog/using-covid-19-pubseq-part1.html index deeb749..454eeb5 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> -<!-- 2020-08-26 Wed 05:02 --> +<!-- 2020-10-26 Mon 05:22 --> <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 - query metadata (part 1)</title> @@ -40,7 +40,7 @@ } pre.src { position: relative; - overflow: visible; + overflow: auto; padding-top: 1.2em; } pre.src:before { @@ -195,50 +195,26 @@ </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. -*/ +// @license magnet:?xt=urn:btih:e95b018ef3580986a04669f1b5879592219e2a7a&dn=public-domain.txt Public Domain <!--/*--><![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; - } -/*]]>*///--> + function CodeHighlightOn(elem, id) + { + var target = document.getElementById(id); + if(null != target) { + elem.classList.add("code-highlighted"); + target.classList.add("code-highlighted"); + } + } + function CodeHighlightOff(elem, id) + { + var target = document.getElementById(id); + if(null != target) { + elem.classList.remove("code-highlighted"); + target.classList.remove("code-highlighted"); + } + } + /*]]>*///--> +// @license-end </script> </head> <body> @@ -248,20 +224,20 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#orga5382ca">1. What does this mean?</a></li> -<li><a href="#orgf6c7763">2. Fetch sequence data</a></li> -<li><a href="#org228a8d5">3. Predicates</a></li> -<li><a href="#orgfb34172">4. Fetch submitter info and other metadata</a></li> -<li><a href="#org16f6b8d">5. Fetch all sequences from Washington state</a></li> -<li><a href="#org2a85986">6. Discussion</a></li> -<li><a href="#orgcf3645c">7. Acknowledgements</a></li> +<li><a href="#org8d34f90">1. What does this mean?</a></li> +<li><a href="#orgc40ff7e">2. Fetch sequence data</a></li> +<li><a href="#orgc6519bc">3. Predicates</a></li> +<li><a href="#orgbb4bffc">4. Fetch submitter info and other metadata</a></li> +<li><a href="#orgae8b515">5. Fetch all sequences from Washington state</a></li> +<li><a href="#org74c9c22">6. Discussion</a></li> +<li><a href="#org26808ce">7. Acknowledgements</a></li> </ul> </div> </div> -<div id="outline-container-orga5382ca" class="outline-2"> -<h2 id="orga5382ca"><span class="section-number-2">1</span> What does this mean?</h2> +<div id="outline-container-org8d34f90" class="outline-2"> +<h2 id="org8d34f90"><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 @@ -313,11 +289,11 @@ initiative! </div> </div> -<div id="outline-container-orgf6c7763" class="outline-2"> -<h2 id="orgf6c7763"><span class="section-number-2">2</span> Fetch sequence data</h2> +<div id="outline-container-orgc40ff7e" class="outline-2"> +<h2 id="orgc40ff7e"><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 +The latest run of the pipeline can be viewed <a href="http://covid19.genenetwork.org/status">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, @@ -338,8 +314,8 @@ these identifiers throughout. </div> </div> -<div id="outline-container-org228a8d5" class="outline-2"> -<h2 id="org228a8d5"><span class="section-number-2">3</span> Predicates</h2> +<div id="outline-container-orgc6519bc" class="outline-2"> +<h2 id="orgc6519bc"><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 @@ -452,8 +428,8 @@ Run this <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&q </div> </div> -<div id="outline-container-orgfb34172" class="outline-2"> -<h2 id="orgfb34172"><span class="section-number-2">4</span> Fetch submitter info and other metadata</h2> +<div id="outline-container-orgbb4bffc" class="outline-2"> +<h2 id="orgbb4bffc"><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 datasets with submitters we can do the above @@ -558,26 +534,94 @@ PREFIX sio: <http://semanticscience.org/resource/"> sio: <http://semantics </div> <p> -Run <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=%0D%0APREFIX+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>. +Run this <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=%0D%0APREFIX+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>. </p> <p> This query 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> using the -<a href="http://identifiers.org/insdc/MT326090.1">http://identifiers.org/insdc/MT326090.1</a> link. +We have also added country and label data to make it a bit easier to +view/query the database and place the sequence on the <a href="http://covid19.genenetwork.org/">map</a>. We use +wikidata entities for disambiguation. By using 'Q30' for the USA we +don't have to figure out the different ways people spell the name. To +get from the wikidata entity to a human readable form we provide a +country name <a href="https://github.com/arvados/bh20-seq-resource/blob/72369b2e2e3cd881be2bd648a61e1449ffe34875/semantic_enrichment/countries.ttl#L306">translation</a> for convenience. For example when the +predicate is <a href="http://purl.obolibrary.org/obo/GAZ_00000448">http://purl.obolibrary.org/obo/GAZ_00000448</a> we can do +</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/> +select distinct ?sample ?geoname +{ + ?sample sio:SIO_000115 "MT326090.1" . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448"><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/> +select distinct ?sample ?geoname +{ + ?sample sio:SIO_000115 "MT326090.1" . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> +PREFIX sio: <http://semanticscience.org/resource/> +select distinct ?sample ?geoname +{ + ?sample sio:SIO_000115 "MT326090.1" . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448">#MainSchema/> +</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> +PREFIX sio: <http://semanticscience.org/resource/> +select distinct ?sample ?geoname +{ + ?sample sio:SIO_000115 "MT326090.1" . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448">PREFIX</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> +PREFIX sio: <http://semanticscience.org/resource/> +select distinct ?sample ?geoname +{ + ?sample sio:SIO_000115 "MT326090.1" . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448"> sio: <http://semanticscience.org/resource/> +</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> +PREFIX sio: <http://semanticscience.org/resource/> +select distinct ?sample ?geoname +{ + ?sample sio:SIO_000115 "MT326090.1" . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448">select</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> +PREFIX sio: <http://semanticscience.org/resource/> +select distinct ?sample ?geoname +{ + ?sample sio:SIO_000115 "MT326090.1" . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448"> </a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> +PREFIX sio: <http://semanticscience.org/resource/> +select distinct ?sample ?geoname +{ + ?sample sio:SIO_000115 "MT326090.1" . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448">distinct</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> +PREFIX sio: <http://semanticscience.org/resource/> +select distinct ?sample ?geoname +{ + ?sample sio:SIO_000115 "MT326090.1" . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448"> ?sample ?geoname +{ + ?sample sio:SIO_000115 "MT326090.1" . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448></a> ?geo . + ?geo rdfs:label ?geoname . +} +</pre> +</div> + +<p> +Which will show the geoname spelled out as 'United States'. </p> <p> -We have also added country and label data to make it a bit easier -to view/query the database and place the sequence on the <a href="http://covid19.genenetwork.org/">map</a>. +For this sample we can also track it back to the original GenBank +<a href="http://identifiers.org/insdc/MT326090.1#sequence">submission</a> using the listed <a href="http://identifiers.org/insdc/MT326090.1">http://identifiers.org/insdc/MT326090.1</a> +link. </p> </div> </div> -<div id="outline-container-org16f6b8d" class="outline-2"> -<h2 id="org16f6b8d"><span class="section-number-2">5</span> Fetch all sequences from Washington state</h2> + +<div id="outline-container-orgae8b515" class="outline-2"> +<h2 id="orgae8b515"><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 @@ -585,19 +629,72 @@ 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 +<pre class="src src-sql"><span style="color: #fff59d;">select</span> ?<span style="color: #84ffff;">date</span> ?<span style="color: #fff59d;">name</span> ?identifier ?seq { ?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> -} + + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223> . + ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date . + ?sample <http://semanticscience.org/resource/SIO_000115> ?name . + ?sample <http://edamontology.org/data_2091"><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> . + ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date . + ?sample <http://semanticscience.org/resource/SIO_000115> ?name . + ?sample <http://edamontology.org/data_2091">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> . + ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date . + ?sample <http://semanticscience.org/resource/SIO_000115> ?name . + ?sample <http://edamontology.org/data_2091">#MainSchema/sample> ?sample . + + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223> . + ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?</a><span style="color: #84ffff;"><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> . + ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date . + ?sample <http://semanticscience.org/resource/SIO_000115> ?name . + ?sample <http://edamontology.org/data_2091">date</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> . + ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date . + ?sample <http://semanticscience.org/resource/SIO_000115> ?name . + ?sample <http://edamontology.org/data_2091"> . + ?sample <http://semanticscience.org/resource/SIO_000115> ?</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> . + ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date . + ?sample <http://semanticscience.org/resource/SIO_000115> ?name . + ?sample <http://edamontology.org/data_2091">name</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> . + ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date . + ?sample <http://semanticscience.org/resource/SIO_000115> ?name . + ?sample <http://edamontology.org/data_2091"> . + ?sample <http://edamontology.org/data_2091></a> ?identifier . +} <span style="color: #fff59d;">order</span> <span style="color: #fff59d;">by</span> ?<span style="color: #84ffff;">date</span> </pre> </div> <p> -which lists 300 sequences originating from Washington state! Which in +Run <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=select+%3Fdate+%3Fname+%3Fidentifier+%3Fseq%0D%0A%7B%0D%0A++++%3Fseq+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2Fsample%3E+%3Fsample+.%0D%0A%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGAZ_00000448%3E+%3Chttp%3A%2F%2Fwww.wikidata.org%2Fentity%2FQ1223%3E+.%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25164%3E+%3Fdate+.%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000115%3E+%3Fname+.%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fedamontology.org%2Fdata_2091%3E+%3Fidentifier+.%0D%0A%7D+order+by+%3Fdate&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+">query</a> +</p> + +<p> +Which shows the date and links to NCBI and raw sequence data in FASTA format, +e.g. +</p> + +<pre class="example" id="orgbdf21bd"> +"date" "name" "identifier" "seq" +"2020-01-15" "MT252760.1" "http://identifiers.org/insdc/MT252760.1#sequence" "http://collections.lugli.arvadosapi.com/c=0164784cba5e3e39b7ba8d83fdc92649+126/sequence.fasta" +"2020-01-15" "MT252720.1" "http://identifiers.org/insdc/MT252720.1#sequence" "http://collections.lugli.arvadosapi.com/c=0387a3e47dd8a0c9ea0a4a21931f6308+126/sequence.fasta" +(...) +</pre> + + +<p> +The query lists 300 sequences originating from Washington state! Which in April was almost half of the set coming out of GenBank. </p> @@ -624,8 +721,8 @@ Run <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&query= </div> </div> -<div id="outline-container-org2a85986" class="outline-2"> -<h2 id="org2a85986"><span class="section-number-2">6</span> Discussion</h2> +<div id="outline-container-org74c9c22" class="outline-2"> +<h2 id="org74c9c22"><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 @@ -636,8 +733,8 @@ referenced in publications and origins are citeable. </div> </div> -<div id="outline-container-orgcf3645c" class="outline-2"> -<h2 id="orgcf3645c"><span class="section-number-2">7</span> Acknowledgements</h2> +<div id="outline-container-org26808ce" class="outline-2"> +<h2 id="org26808ce"><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 @@ -652,7 +749,7 @@ 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 2020-08-26 Wed 05:02</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 2020-10-26 Mon 05:21</small>. </div> </body> </html> diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org index e41952d..78d9f19 100644 --- a/doc/blog/using-covid-19-pubseq-part1.org +++ b/doc/blog/using-covid-19-pubseq-part1.org @@ -62,7 +62,7 @@ initiative! * Fetch sequence data -The latest run of the pipeline can be viewed [[https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca][here]]. Each of these +The latest run of the pipeline can be viewed [[http://covid19.genenetwork.org/status][here]]. Each of these generated files can just be downloaded for your own use and sharing! Data is published under a [[https://creativecommons.org/licenses/by/4.0/][Creative Commons 4.0 attribution license]] (CC-BY-4.0). This means that, unlike some other 'public' resources, @@ -241,16 +241,36 @@ select distinct ?sample ?p ?o } #+end_src -Run [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=%0D%0APREFIX+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]]. +Run this [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=%0D%0APREFIX+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]]. This query tells us the sample was submitted "2020-03-21" and originates from http://www.wikidata.org/entity/Q30, 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 [[http://identifiers.org/insdc/MT326090.1#sequence][submission]] using the -http://identifiers.org/insdc/MT326090.1 link. +We have also added country and label data to make it a bit easier to +view/query the database and place the sequence on the [[http://covid19.genenetwork.org/][map]]. We use +wikidata entities for disambiguation. By using 'Q30' for the USA we +don't have to figure out the different ways people spell the name. To +get from the wikidata entity to a human readable form we provide a +country name [[https://github.com/arvados/bh20-seq-resource/blob/72369b2e2e3cd881be2bd648a61e1449ffe34875/semantic_enrichment/countries.ttl#L306][translation]] for convenience. For example when the +predicate is http://purl.obolibrary.org/obo/GAZ_00000448 we can do + +#+begin_src sql +PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +PREFIX sio: <http://semanticscience.org/resource/> +select distinct ?sample ?geoname +{ + ?sample sio:SIO_000115 "MT326090.1" . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> ?geo . + ?geo rdfs:label ?geoname . +} +#+end_src + +Which will show the geoname spelled out as 'United States'. + +For this sample we can also track it back to the original GenBank +[[http://identifiers.org/insdc/MT326090.1#sequence][submission]] using the listed http://identifiers.org/insdc/MT326090.1 +link. -We have also added country and label data to make it a bit easier -to view/query the database and place the sequence on the [[http://covid19.genenetwork.org/][map]]. * Fetch all sequences from Washington state @@ -258,14 +278,31 @@ 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 #+begin_src sql -select ?seq ?sample +select ?date ?name ?identifier ?seq { ?seq <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . - ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223> -} + + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223> . + ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date . + ?sample <http://semanticscience.org/resource/SIO_000115> ?name . + ?sample <http://edamontology.org/data_2091> ?identifier . +} order by ?date #+end_src -which lists 300 sequences originating from Washington state! Which in +Run [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=select+%3Fdate+%3Fname+%3Fidentifier+%3Fseq%0D%0A%7B%0D%0A++++%3Fseq+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2Fsample%3E+%3Fsample+.%0D%0A%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGAZ_00000448%3E+%3Chttp%3A%2F%2Fwww.wikidata.org%2Fentity%2FQ1223%3E+.%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25164%3E+%3Fdate+.%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000115%3E+%3Fname+.%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fedamontology.org%2Fdata_2091%3E+%3Fidentifier+.%0D%0A%7D+order+by+%3Fdate&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][query]] + +Which shows the date and links to NCBI and raw sequence data in FASTA format, +e.g. + +#+begin_example +"date" "name" "identifier" "seq" +"2020-01-15" "MT252760.1" "http://identifiers.org/insdc/MT252760.1#sequence" "http://collections.lugli.arvadosapi.com/c=0164784cba5e3e39b7ba8d83fdc92649+126/sequence.fasta" +"2020-01-15" "MT252720.1" "http://identifiers.org/insdc/MT252720.1#sequence" "http://collections.lugli.arvadosapi.com/c=0387a3e47dd8a0c9ea0a4a21931f6308+126/sequence.fasta" +(...) +#+end_example + + +The query lists 300 sequences originating from Washington state! Which in April was almost half of the set coming out of GenBank. Likewise to list all sequences from Turkey we can find the wikidata |