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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 5e52b82..1959fac 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 10:12 --> +<!-- 2020-05-29 Fri 12:06 --> <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> @@ -242,40 +242,26 @@ for the JavaScript code in this tag. </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"> +<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> +<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> </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 id="outline-container-org9afe6ab" class="outline-2"> +<h2 id="org9afe6ab"><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 @@ -328,8 +314,8 @@ initiative! </div> -<div id="outline-container-org038e367" class="outline-2"> -<h2 id="org038e367"><span class="section-number-2">2</span> Fetch sequence data</h2> +<div id="outline-container-orgf4bc3d4" class="outline-2"> +<h2 id="orgf4bc3d4"><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 @@ -353,8 +339,8 @@ these identifiers throughout. </div> </div> -<div id="outline-container-org3ad046c" class="outline-2"> -<h2 id="org3ad046c"><span class="section-number-2">3</span> Predicates</h2> +<div id="outline-container-org9d7d482" class="outline-2"> +<h2 id="org9d7d482"><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 @@ -464,8 +450,8 @@ Now we got this far, lets <a href="http://sparql.genenetwork.org/sparql/?default </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 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 class="outline-text-2" id="text-4"> <p> To get dataests with submitters we can do the above @@ -575,8 +561,8 @@ to view/query the database. </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 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 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 @@ -603,8 +589,8 @@ half of the set coming out of GenBank. </div> </div> -<div id="outline-container-orgbc80874" class="outline-2"> -<h2 id="orgbc80874"><span class="section-number-2">6</span> Discussion</h2> +<div id="outline-container-org7060f51" class="outline-2"> +<h2 id="org7060f51"><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 @@ -615,8 +601,8 @@ referenced in publications and origins are citeable. </div> </div> -<div id="outline-container-orgce8eaf6" class="outline-2"> -<h2 id="orgce8eaf6"><span class="section-number-2">7</span> Acknowledgements</h2> +<div id="outline-container-orgdc51ccc" class="outline-2"> +<h2 id="orgdc51ccc"><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 @@ -631,7 +617,7 @@ 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 10:12</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 12:06</small>. </div> </body> </html> |