diff options
Diffstat (limited to 'doc')
-rw-r--r-- | doc/blog/using-covid-19-pubseq-part2.html | 394 | ||||
-rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.html | 296 | ||||
-rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.org | 116 | ||||
-rw-r--r-- | doc/blog/using-covid-19-pubseq-part4.html | 266 | ||||
-rw-r--r-- | doc/blog/using-covid-19-pubseq-part4.org | 3 | ||||
-rw-r--r-- | doc/blog/using-covid-19-pubseq-part5.html | 277 | ||||
-rw-r--r-- | doc/blog/using-covid-19-pubseq-part5.org | 17 |
7 files changed, 1260 insertions, 109 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part2.html b/doc/blog/using-covid-19-pubseq-part2.html new file mode 100644 index 0000000..c047441 --- /dev/null +++ b/doc/blog/using-covid-19-pubseq-part2.html @@ -0,0 +1,394 @@ +<?xml version="1.0" encoding="utf-8"?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" +"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> +<head> +<!-- 2020-05-30 Sat 11:50 --> +<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 2)</title> +<meta name="generator" content="Org mode" /> +<meta name="author" content="Pjotr Prins" /> +<style type="text/css"> + <!--/*--><![CDATA[/*><!--*/ + .title { text-align: center; + margin-bottom: .2em; } + .subtitle { text-align: center; + font-size: medium; + font-weight: bold; + margin-top:0; } + .todo { font-family: monospace; color: red; } + .done { font-family: monospace; color: green; } + .priority { font-family: monospace; color: orange; } + .tag { background-color: #eee; font-family: monospace; + padding: 2px; font-size: 80%; font-weight: normal; } + .timestamp { color: #bebebe; } + .timestamp-kwd { color: #5f9ea0; } + .org-right { margin-left: auto; margin-right: 0px; text-align: right; } + .org-left { margin-left: 0px; margin-right: auto; text-align: left; } + .org-center { margin-left: auto; margin-right: auto; text-align: center; } + .underline { text-decoration: underline; } + #postamble p, #preamble p { font-size: 90%; margin: .2em; } + p.verse { margin-left: 3%; } + pre { + border: 1px solid #ccc; + box-shadow: 3px 3px 3px #eee; + padding: 8pt; + font-family: monospace; + overflow: auto; + margin: 1.2em; + } + pre.src { + position: relative; + overflow: visible; + padding-top: 1.2em; + } + pre.src:before { + display: none; + position: absolute; + background-color: white; + top: -10px; + right: 10px; + padding: 3px; + border: 1px solid black; + } + pre.src:hover:before { display: inline;} + /* Languages per Org manual */ + pre.src-asymptote:before { content: 'Asymptote'; } + pre.src-awk:before { content: 'Awk'; } + pre.src-C:before { content: 'C'; } + /* pre.src-C++ doesn't work in CSS */ + pre.src-clojure:before { content: 'Clojure'; } + pre.src-css:before { content: 'CSS'; } + pre.src-D:before { content: 'D'; } + pre.src-ditaa:before { content: 'ditaa'; } + pre.src-dot:before { content: 'Graphviz'; } + pre.src-calc:before { content: 'Emacs Calc'; } + pre.src-emacs-lisp:before { content: 'Emacs Lisp'; } + pre.src-fortran:before { content: 'Fortran'; } + pre.src-gnuplot:before { content: 'gnuplot'; } + pre.src-haskell:before { content: 'Haskell'; } + pre.src-hledger:before { content: 'hledger'; } + pre.src-java:before { content: 'Java'; } + pre.src-js:before { content: 'Javascript'; } + pre.src-latex:before { content: 'LaTeX'; } + pre.src-ledger:before { content: 'Ledger'; } + pre.src-lisp:before { content: 'Lisp'; } + pre.src-lilypond:before { content: 'Lilypond'; } + pre.src-lua:before { content: 'Lua'; } + pre.src-matlab:before { content: 'MATLAB'; } + pre.src-mscgen:before { content: 'Mscgen'; } + pre.src-ocaml:before { content: 'Objective Caml'; } + pre.src-octave:before { content: 'Octave'; } + pre.src-org:before { content: 'Org mode'; } + pre.src-oz:before { content: 'OZ'; } + pre.src-plantuml:before { content: 'Plantuml'; } + pre.src-processing:before { content: 'Processing.js'; } + pre.src-python:before { content: 'Python'; } + pre.src-R:before { content: 'R'; } + pre.src-ruby:before { content: 'Ruby'; } + pre.src-sass:before { content: 'Sass'; } + pre.src-scheme:before { content: 'Scheme'; } + pre.src-screen:before { content: 'Gnu Screen'; } + pre.src-sed:before { content: 'Sed'; } + pre.src-sh:before { content: 'shell'; } + pre.src-sql:before { content: 'SQL'; } + pre.src-sqlite:before { content: 'SQLite'; } + /* additional languages in org.el's org-babel-load-languages alist */ + pre.src-forth:before { content: 'Forth'; } + pre.src-io:before { content: 'IO'; } + pre.src-J:before { content: 'J'; } + pre.src-makefile:before { content: 'Makefile'; } + pre.src-maxima:before { content: 'Maxima'; } + pre.src-perl:before { content: 'Perl'; } + pre.src-picolisp:before { content: 'Pico Lisp'; } + pre.src-scala:before { content: 'Scala'; } + pre.src-shell:before { content: 'Shell Script'; } + pre.src-ebnf2ps:before { content: 'ebfn2ps'; } + /* additional language identifiers per "defun org-babel-execute" + in ob-*.el */ + pre.src-cpp:before { content: 'C++'; } + pre.src-abc:before { content: 'ABC'; } + pre.src-coq:before { content: 'Coq'; } + pre.src-groovy:before { content: 'Groovy'; } + /* additional language identifiers from org-babel-shell-names in + ob-shell.el: ob-shell is the only babel language using a lambda to put + the execution function name together. */ + pre.src-bash:before { content: 'bash'; } + pre.src-csh:before { content: 'csh'; } + pre.src-ash:before { content: 'ash'; } + pre.src-dash:before { content: 'dash'; } + pre.src-ksh:before { content: 'ksh'; } + pre.src-mksh:before { content: 'mksh'; } + pre.src-posh:before { content: 'posh'; } + /* Additional Emacs modes also supported by the LaTeX listings package */ + pre.src-ada:before { content: 'Ada'; } + pre.src-asm:before { content: 'Assembler'; } + pre.src-caml:before { content: 'Caml'; } + pre.src-delphi:before { content: 'Delphi'; } + pre.src-html:before { content: 'HTML'; } + pre.src-idl:before { content: 'IDL'; } + pre.src-mercury:before { content: 'Mercury'; } + pre.src-metapost:before { content: 'MetaPost'; } + pre.src-modula-2:before { content: 'Modula-2'; } + pre.src-pascal:before { content: 'Pascal'; } + pre.src-ps:before { content: 'PostScript'; } + pre.src-prolog:before { content: 'Prolog'; } + pre.src-simula:before { content: 'Simula'; } + pre.src-tcl:before { content: 'tcl'; } + pre.src-tex:before { content: 'TeX'; } + pre.src-plain-tex:before { content: 'Plain TeX'; } + pre.src-verilog:before { content: 'Verilog'; } + pre.src-vhdl:before { content: 'VHDL'; } + pre.src-xml:before { content: 'XML'; } + pre.src-nxml:before { content: 'XML'; } + /* add a generic configuration mode; LaTeX export needs an additional + (add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */ + pre.src-conf:before { content: 'Configuration File'; } + + table { border-collapse:collapse; } + caption.t-above { caption-side: top; } + caption.t-bottom { caption-side: bottom; } + td, th { vertical-align:top; } + th.org-right { text-align: center; } + th.org-left { text-align: center; } + th.org-center { text-align: center; } + td.org-right { text-align: right; } + td.org-left { text-align: left; } + td.org-center { text-align: center; } + dt { font-weight: bold; } + .footpara { display: inline; } + .footdef { margin-bottom: 1em; } + .figure { padding: 1em; } + .figure p { text-align: center; } + .equation-container { + display: table; + text-align: center; + width: 100%; + } + .equation { + vertical-align: middle; + } + .equation-label { + display: table-cell; + text-align: right; + vertical-align: middle; + } + .inlinetask { + padding: 10px; + border: 2px solid gray; + margin: 10px; + background: #ffffcc; + } + #org-div-home-and-up + { text-align: right; font-size: 70%; white-space: nowrap; } + textarea { overflow-x: auto; } + .linenr { font-size: smaller } + .code-highlighted { background-color: #ffff00; } + .org-info-js_info-navigation { border-style: none; } + #org-info-js_console-label + { font-size: 10px; font-weight: bold; white-space: nowrap; } + .org-info-js_search-highlight + { background-color: #ffff00; color: #000000; font-weight: bold; } + .org-svg { width: 90%; } + /*]]>*/--> +</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. +*/ +<!--/*--><![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; + } +/*]]>*///--> +</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 2)</h1> +<div id="table-of-contents"> +<h2>Table of Contents</h2> +<div id="text-table-of-contents"> +<ul> +<li><a href="#org7942167">1. Finding output of workflows</a></li> +<li><a href="#org0022bbe">2. Introduction</a></li> +<li><a href="#org3929710">3. The Arvados file interface</a></li> +<li><a href="#orgc4dba6e">4. Using the Arvados API</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-org7942167" class="outline-2"> +<h2 id="org7942167"><span class="section-number-2">1</span> Finding output of workflows</h2> +<div class="outline-text-2" id="text-1"> +<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> +</div> + +<div id="outline-container-org0022bbe" class="outline-2"> +<h2 id="org0022bbe"><span class="section-number-2">2</span> Introduction</h2> +<div class="outline-text-2" id="text-2"> +<p> +We are using Arvados to run common workflow language (CWL) pipelines. +The most recent output is on display on a <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">web page</a> (with time stamp) +and a full list is generated <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">here</a>. It is nice to start up, but for +most users we need a dedicated and themed results page. People don't +want to wade through thousands of output files! +</p> +</div> +</div> + +<div id="outline-container-org3929710" class="outline-2"> +<h2 id="org3929710"><span class="section-number-2">3</span> The Arvados file interface</h2> +<div class="outline-text-2" id="text-3"> +<p> +Arvados has the web server, but it also has a REST API and associated +command line tools. We are already using the <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/main.py#L27">API</a> to upload data. If +you follow the pip or <a href="../INSTALL.md">../INSTALL.md</a> GNU Guix instructions for +installing Arvados API you'll find the following command line tools +(also documented <a href="https://doc.arvados.org/v2.0/sdk/cli/subcommands.html">here</a>): +</p> + +<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> + + +<colgroup> +<col class="org-left" /> + +<col class="org-left" /> +</colgroup> +<thead> +<tr> +<th scope="col" class="org-left">Command</th> +<th scope="col" class="org-left">Description</th> +</tr> +</thead> +<tbody> +<tr> +<td class="org-left">arv-ls</td> +<td class="org-left">list files in Arvados</td> +</tr> + +<tr> +<td class="org-left">arv-put</td> +<td class="org-left">upload a file to Arvados</td> +</tr> + +<tr> +<td class="org-left">arv-get</td> +<td class="org-left">get a textual representation of Arvados objects from the command line. The output can be limited to a subset of the object’s fields. This command can be used with only the knowledge of an object’s UUID</td> +</tr> +</tbody> +</table> + +<p> +Now, this is a public instance so we can use the tokens from +the <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/main.py#L16">uploader</a>. +</p> + +<div class="SOURCE"> +<p> +export ARVADOS<sub>API</sub><sub>HOST</sub>='lugli.arvadosapi.com' +export ARVADOS<sub>API</sub><sub>TOKEN</sub>='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' +arv-ls lugli-4zz18-z513nlpqm03hpca +</p> + +</div> + +<p> +will list all files (the UUID we got from the Arvados results page). To +get the UUID of the files +</p> + +<div class="SOURCE"> +<p> +curl <a href="https://lugli.arvadosapi.com/arvados/v1/config">https://lugli.arvadosapi.com/arvados/v1/config</a> | jq .Users.AnonymousUserToken +env ARVADOS<sub>API</sub><sub>TOKEN</sub>=5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh \ + arv-get lugli-4zz18-z513nlpqm03hpca +</p> + +</div> + +<p> +and fetch one listed JSON file <code>chunk001_bin4000.schematic.json</code> with +its listed UUID: +</p> + +<pre class="example"> +arv-get 2be6af7b4741f2a5c5f8ff2bc6152d73+1955623+Ab9ad65d7fe958a053b3a57d545839de18290843a@5ed7f3c5 +</pre> +</div> +</div> + +<div id="outline-container-orgc4dba6e" class="outline-2"> +<h2 id="orgc4dba6e"><span class="section-number-2">4</span> Using the Arvados API</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 2020-05-30 Sat 11:50</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 4132784..91879b0 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> -<!-- 2020-05-30 Sat 10:45 --> +<!-- 2020-05-30 Sat 18:12 --> <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> @@ -248,64 +248,62 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org7fda7c8">1. Uploading Data</a></li> -<li><a href="#orgb062ac0">2. Introduction</a></li> -<li><a href="#org4061598">3. Step 1: Upload sequence</a></li> -<li><a href="#org51d80f8">4. Step 2: Add metadata</a> +<li><a href="#org193669a">1. Uploading Data</a></li> +<li><a href="#orgc6b3a47">2. Step 1: Upload sequence</a></li> +<li><a href="#org9c08714">3. Step 2: Add metadata</a> <ul> -<li><a href="#orgbb8f0bb">4.1. Obligatory fields</a> +<li><a href="#org4c2e907">3.1. Obligatory fields</a> <ul> -<li><a href="#org0e615dc">4.1.1. Sample ID (sample<sub>id</sub>)</a></li> -<li><a href="#org4d5308a">4.1.2. Collection date</a></li> -<li><a href="#org429f153">4.1.3. Collection location</a></li> -<li><a href="#orgbd7fa51">4.1.4. Sequencing technology</a></li> -<li><a href="#orgc3b424f">4.1.5. Authors</a></li> +<li><a href="#orgdddcb2e">3.1.1. Sample ID (sample<sub>id</sub>)</a></li> +<li><a href="#orge9c2e76">3.1.2. Collection date</a></li> +<li><a href="#org62c55ce">3.1.3. Collection location</a></li> +<li><a href="#org460b377">3.1.4. Sequencing technology</a></li> +<li><a href="#org77b1e14">3.1.5. Authors</a></li> </ul> </li> -<li><a href="#org5c01347">4.2. Optional fields</a> +<li><a href="#org3cb346f">3.2. Optional fields</a> <ul> -<li><a href="#org7fc5461">4.2.1. Host information</a></li> -<li><a href="#org140c8b5">4.2.2. Collecting institution</a></li> -<li><a href="#orgf231cf9">4.2.3. Specimen source</a></li> -<li><a href="#org74de839">4.2.4. Source database accession</a></li> -<li><a href="#org8927a67">4.2.5. Strain name</a></li> +<li><a href="#orgb0cffbb">3.2.1. Host information</a></li> +<li><a href="#orgd2a43a6">3.2.2. Collecting institution</a></li> +<li><a href="#org8d5bcf7">3.2.3. Specimen source</a></li> +<li><a href="#org86b21b2">3.2.4. Source database accession</a></li> +<li><a href="#org771ea66">3.2.5. Strain name</a></li> </ul> </li> </ul> </li> -<li><a href="#org38d48d8">5. Step 3: Submit to COVID-19 PubSeq</a></li> -<li><a href="#org5ec1337">6. Step 4: Check output</a> +<li><a href="#org7d281f5">4. Step 3: Submit to COVID-19 PubSeq</a> <ul> -<li><a href="#org070e13e">6.1. Trouble shooting</a></li> +<li><a href="#orgdf0f02d">4.1. Trouble shooting</a></li> +</ul> +</li> +<li><a href="#org29f8a92">5. Step 4: Check output</a></li> +<li><a href="#orgf493854">6. Bulk sequence uploader</a> +<ul> +<li><a href="#org37fadbc">6.1. Run the uploader (CLI)</a></li> +<li><a href="#org39adf09">6.2. Example: uploading bulk GenBank sequences</a></li> </ul> </li> </ul> </div> </div> -<div id="outline-container-org7fda7c8" class="outline-2"> -<h2 id="org7fda7c8"><span class="section-number-2">1</span> Uploading Data</h2> -<div class="outline-text-2" id="text-1"> -<p> -<i>Work in progress!</i> -</p> -</div> -</div> -<div id="outline-container-orgb062ac0" class="outline-2"> -<h2 id="orgb062ac0"><span class="section-number-2">2</span> Introduction</h2> -<div class="outline-text-2" id="text-2"> + +<div id="outline-container-org193669a" class="outline-2"> +<h2 id="org193669a"><span class="section-number-2">1</span> Uploading Data</h2> +<div class="outline-text-2" id="text-1"> <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. +public resource for global comparisons. A recompute of the pangenome +gets triggered on upload. Read the <a href="./about">ABOUT</a> page for more information. </p> </div> </div> -<div id="outline-container-org4061598" class="outline-2"> -<h2 id="org4061598"><span class="section-number-2">3</span> Step 1: Upload sequence</h2> -<div class="outline-text-2" id="text-3"> +<div id="outline-container-orgc6b3a47" class="outline-2"> +<h2 id="orgc6b3a47"><span class="section-number-2">2</span> Step 1: Upload sequence</h2> +<div class="outline-text-2" id="text-2"> <p> To upload a sequence in the <a href="http://covid19.genenetwork.org/">web upload page</a> hit the browse button and select the FASTA file on your local hard disk. @@ -332,9 +330,9 @@ an improved pangenome. </div> </div> -<div id="outline-container-org51d80f8" class="outline-2"> -<h2 id="org51d80f8"><span class="section-number-2">4</span> Step 2: Add metadata</h2> -<div class="outline-text-2" id="text-4"> +<div id="outline-container-org9c08714" class="outline-2"> +<h2 id="org9c08714"><span class="section-number-2">3</span> Step 2: Add metadata</h2> +<div class="outline-text-2" id="text-3"> <p> The <a href="./">web upload page</a> contains fields for adding metadata. Metadata is not only important for attribution, is also important for @@ -348,7 +346,7 @@ A number of fields are obligatory: sample id, date, location, technology and authors. The others are optional, but it is valuable to enter them when information is available. Metadata is defined in this <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml">schema</a>. From this schema we generate the input form. Note that -opitional fields have a question mark in the <code>type</code>. You can add +optional fields have a question mark in the <code>type</code>. You can add metadata yourself, btw, because this is a public resource! See also <a href="./blog?id=using-covid-19-pubseq-part5">Modify metadata</a> for more information. </p> @@ -359,13 +357,13 @@ the web form. Here we add some extra information. </p> </div> -<div id="outline-container-orgbb8f0bb" class="outline-3"> -<h3 id="orgbb8f0bb"><span class="section-number-3">4.1</span> Obligatory fields</h3> -<div class="outline-text-3" id="text-4-1"> +<div id="outline-container-org4c2e907" class="outline-3"> +<h3 id="org4c2e907"><span class="section-number-3">3.1</span> Obligatory fields</h3> +<div class="outline-text-3" id="text-3-1"> </div> -<div id="outline-container-org0e615dc" class="outline-4"> -<h4 id="org0e615dc"><span class="section-number-4">4.1.1</span> Sample ID (sample<sub>id</sub>)</h4> -<div class="outline-text-4" id="text-4-1-1"> +<div id="outline-container-orgdddcb2e" class="outline-4"> +<h4 id="orgdddcb2e"><span class="section-number-4">3.1.1</span> Sample ID (sample<sub>id</sub>)</h4> +<div class="outline-text-4" id="text-3-1-1"> <p> This is a string field that defines a unique sample identifier by the submitter. In addition to sample<sub>id</sub> we also have host<sub>id</sub>, @@ -382,37 +380,37 @@ Here we add the GenBank ID MT536190.1. </div> </div> -<div id="outline-container-org4d5308a" class="outline-4"> -<h4 id="org4d5308a"><span class="section-number-4">4.1.2</span> Collection date</h4> -<div class="outline-text-4" id="text-4-1-2"> +<div id="outline-container-orge9c2e76" class="outline-4"> +<h4 id="orge9c2e76"><span class="section-number-4">3.1.2</span> Collection date</h4> +<div class="outline-text-4" id="text-3-1-2"> <p> Estimated collection date. The GenBank page says April 6, 2020. </p> </div> </div> -<div id="outline-container-org429f153" class="outline-4"> -<h4 id="org429f153"><span class="section-number-4">4.1.3</span> Collection location</h4> -<div class="outline-text-4" id="text-4-1-3"> +<div id="outline-container-org62c55ce" class="outline-4"> +<h4 id="org62c55ce"><span class="section-number-4">3.1.3</span> Collection location</h4> +<div class="outline-text-4" id="text-3-1-3"> <p> -A search on wikidata says Los Angelos is +A search on wikidata says Los Angeles is <a href="https://www.wikidata.org/entity/Q65">https://www.wikidata.org/entity/Q65</a> </p> </div> </div> -<div id="outline-container-orgbd7fa51" class="outline-4"> -<h4 id="orgbd7fa51"><span class="section-number-4">4.1.4</span> Sequencing technology</h4> -<div class="outline-text-4" id="text-4-1-4"> +<div id="outline-container-org460b377" class="outline-4"> +<h4 id="org460b377"><span class="section-number-4">3.1.4</span> Sequencing technology</h4> +<div class="outline-text-4" id="text-3-1-4"> <p> GenBank entry says Illumina, so we can fill that in </p> </div> </div> -<div id="outline-container-orgc3b424f" class="outline-4"> -<h4 id="orgc3b424f"><span class="section-number-4">4.1.5</span> Authors</h4> -<div class="outline-text-4" id="text-4-1-5"> +<div id="outline-container-org77b1e14" class="outline-4"> +<h4 id="org77b1e14"><span class="section-number-4">3.1.5</span> Authors</h4> +<div class="outline-text-4" id="text-3-1-5"> <p> GenBank entry says 'Lamers,S., Nolan,D.J., Rose,R., Cross,S., Moraga Amador,D., Yang,T., Caruso,L., Navia,W., Von Borstel,L., Hui Zhou,X., @@ -422,17 +420,17 @@ Freehan,A. and Garcia-Diaz,J.', so we can fill that in. </div> </div> -<div id="outline-container-org5c01347" class="outline-3"> -<h3 id="org5c01347"><span class="section-number-3">4.2</span> Optional fields</h3> -<div class="outline-text-3" id="text-4-2"> +<div id="outline-container-org3cb346f" class="outline-3"> +<h3 id="org3cb346f"><span class="section-number-3">3.2</span> Optional fields</h3> +<div class="outline-text-3" id="text-3-2"> <p> All other fields are optional. But let's see what we can add. </p> </div> -<div id="outline-container-org7fc5461" class="outline-4"> -<h4 id="org7fc5461"><span class="section-number-4">4.2.1</span> Host information</h4> -<div class="outline-text-4" id="text-4-2-1"> +<div id="outline-container-orgb0cffbb" class="outline-4"> +<h4 id="orgb0cffbb"><span class="section-number-4">3.2.1</span> Host information</h4> +<div class="outline-text-4" id="text-3-2-1"> <p> Sadly, not much is known about the host from GenBank. A little sleuthing renders an interesting paper by some of the authors titled @@ -445,27 +443,27 @@ did to the person and what the person was like (say age group). </div> </div> -<div id="outline-container-org140c8b5" class="outline-4"> -<h4 id="org140c8b5"><span class="section-number-4">4.2.2</span> Collecting institution</h4> -<div class="outline-text-4" id="text-4-2-2"> +<div id="outline-container-orgd2a43a6" class="outline-4"> +<h4 id="orgd2a43a6"><span class="section-number-4">3.2.2</span> Collecting institution</h4> +<div class="outline-text-4" id="text-3-2-2"> <p> We can fill that in. </p> </div> </div> -<div id="outline-container-orgf231cf9" class="outline-4"> -<h4 id="orgf231cf9"><span class="section-number-4">4.2.3</span> Specimen source</h4> -<div class="outline-text-4" id="text-4-2-3"> +<div id="outline-container-org8d5bcf7" class="outline-4"> +<h4 id="org8d5bcf7"><span class="section-number-4">3.2.3</span> Specimen source</h4> +<div class="outline-text-4" id="text-3-2-3"> <p> We have that: nasopharyngeal swab </p> </div> </div> -<div id="outline-container-org74de839" class="outline-4"> -<h4 id="org74de839"><span class="section-number-4">4.2.4</span> Source database accession</h4> -<div class="outline-text-4" id="text-4-2-4"> +<div id="outline-container-org86b21b2" class="outline-4"> +<h4 id="org86b21b2"><span class="section-number-4">3.2.4</span> Source database accession</h4> +<div class="outline-text-4" id="text-3-2-4"> <p> Genbank which is <a href="http://identifiers.org/insdc/MT536190.1#sequence">http://identifiers.org/insdc/MT536190.1#sequence</a>. Note we plug in our own identifier MT536190.1. @@ -473,9 +471,9 @@ Note we plug in our own identifier MT536190.1. </div> </div> -<div id="outline-container-org8927a67" class="outline-4"> -<h4 id="org8927a67"><span class="section-number-4">4.2.5</span> Strain name</h4> -<div class="outline-text-4" id="text-4-2-5"> +<div id="outline-container-org771ea66" class="outline-4"> +<h4 id="org771ea66"><span class="section-number-4">3.2.5</span> Strain name</h4> +<div class="outline-text-4" id="text-3-2-5"> <p> SARS-CoV-2/human/USA/LA-BIE-070/2020 </p> @@ -484,20 +482,36 @@ SARS-CoV-2/human/USA/LA-BIE-070/2020 </div> </div> -<div id="outline-container-org38d48d8" class="outline-2"> -<h2 id="org38d48d8"><span class="section-number-2">5</span> Step 3: Submit to COVID-19 PubSeq</h2> -<div class="outline-text-2" id="text-5"> +<div id="outline-container-org7d281f5" class="outline-2"> +<h2 id="org7d281f5"><span class="section-number-2">4</span> Step 3: Submit to COVID-19 PubSeq</h2> +<div class="outline-text-2" id="text-4"> <p> Once you have the sequence and the metadata together, hit the 'Add to Pangenome' button. The data will be checked, submitted and the workflows should kick in! </p> </div> + + +<div id="outline-container-orgdf0f02d" class="outline-3"> +<h3 id="orgdf0f02d"><span class="section-number-3">4.1</span> Trouble shooting</h3> +<div class="outline-text-3" id="text-4-1"> +<p> +We got an error saying: {"stem": "<a href="http://www.wikidata.org/entity/">http://www.wikidata.org/entity/</a>",… +which means that our location field was not formed correctly! After +fixing it to look like <a href="http://www.wikidata.org/entity/Q65">http://www.wikidata.org/entity/Q65</a> (note http +instead on https and entity instead of wiki) the submission went +through. Reload the page (it won't empty the fields) to re-enable the +submit button. +</p> +</div> +</div> </div> -<div id="outline-container-org5ec1337" class="outline-2"> -<h2 id="org5ec1337"><span class="section-number-2">6</span> Step 4: Check output</h2> -<div class="outline-text-2" id="text-6"> + +<div id="outline-container-org29f8a92" class="outline-2"> +<h2 id="org29f8a92"><span class="section-number-2">5</span> Step 4: Check output</h2> +<div class="outline-text-2" id="text-5"> <p> The current pipeline takes 5.5 hours to complete! Once it completes the updated data can be checked on the <a href="./download">DOWNLOAD</a> page. After completion @@ -505,24 +519,122 @@ of above output this <a href="http://sparql.genenetwork.org/sparql/?default-grap in. </p> </div> +</div> + +<div id="outline-container-orgf493854" class="outline-2"> +<h2 id="orgf493854"><span class="section-number-2">6</span> Bulk sequence uploader</h2> +<div class="outline-text-2" id="text-6"> +<p> +Above steps require a manual upload of one sequence with metadata. +What if you have a number of sequences you want to upload in bulk? +For this we have a command line version of the uploader that can +directly submit to COVID-19 PubSeq. It accepts a FASTA sequence +file an associated metadata in <a href="https://github.com/arvados/bh20-seq-resource/blob/master/example/maximum_metadata_example.yaml">YAML</a> format. The YAML matches +the web form and gets validated from the same <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml">schema</a> looks. The YAML +that you need to create/generate for your samples looks like +</p> + +<div class="org-src-container"> +<pre class="src src-json">id: placeholder + +host: + host_id: XX<span style="color: #8bc34a;">1</span> + host_species: http://purl.obolibrary.org/obo/NCBITaxon_<span style="color: #8bc34a;">9606</span> + host_sex: http://purl.obolibrary.org/obo/PATO_<span style="color: #8bc34a;">0000384</span> + host_age: <span style="color: #8bc34a;">20</span> + host_age_unit: http://purl.obolibrary.org/obo/UO_<span style="color: #8bc34a;">0000036</span> + host_health_status: http://purl.obolibrary.org/obo/NCIT_C<span style="color: #8bc34a;">25269</span> + host_treatment: Process in which the act is intended to modify or alter host status <span style="color: #e91e63;">(</span>Compounds<span style="color: #e91e63;">)</span> + host_vaccination: <span style="color: #e91e63;">[</span>vaccines<span style="color: #8bc34a;">1</span>,vaccine<span style="color: #8bc34a;">2</span><span style="color: #e91e63;">]</span> + ethnicity: http://purl.obolibrary.org/obo/HANCESTRO_<span style="color: #8bc34a;">0010</span> + additional_host_information: Optional free text field for additional information + +sample: + sample_id: Id of the sample as defined by the submitter + collector_name: Name of the person that took the sample + collecting_institution: Institute that was responsible of sampling + specimen_source: <span style="color: #e91e63;">[</span>http://purl.obolibrary.org/obo/NCIT_C<span style="color: #8bc34a;">155831</span>,http://purl.obolibrary.org/obo/NCIT_C<span style="color: #8bc34a;">155835</span>] + collection_date: <span style="color: #9ccc65;">"2020-01-01"</span> + collection_location: http://www.wikidata.org/entity/Q<span style="color: #8bc34a;">148</span> + sample_storage_conditions: frozen specimen + source_database_accession: <span style="color: #2196F3;">[</span>http://identifiers.org/insdc/LC<span style="color: #8bc34a;">522350.1</span>#sequence] + additional_collection_information: Optional free text field for additional information + +virus: + virus_species: http://purl.obolibrary.org/obo/NCBITaxon_<span style="color: #8bc34a;">2697049</span> + virus_strain: SARS-CoV-<span style="color: #8bc34a;">2</span>/human/CHN/HS_<span style="color: #8bc34a;">8</span>/<span style="color: #8bc34a;">2020</span> + +technology: + sample_sequencing_technology: <span style="color: #EF6C00;">[</span>http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0009173</span>,http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0009173</span>] + sequence_assembly_method: Protocol used for assembly + sequencing_coverage: <span style="color: #B388FF;">[</span><span style="color: #8bc34a;">70.0</span>, <span style="color: #8bc34a;">100.0</span><span style="color: #B388FF;">]</span> + additional_technology_information: Optional free text field for additional information + +submitter: + authors: <span style="color: #B388FF;">[</span>John Doe, Joe Boe, Jonny Oe<span style="color: #B388FF;">]</span> + submitter_name: <span style="color: #B388FF;">[</span>John Doe<span style="color: #B388FF;">]</span> + submitter_address: John Doe's address + originating_lab: John Doe kitchen + lab_address: John Doe's address + provider_sample_id: XXX<span style="color: #8bc34a;">1</span> + submitter_sample_id: XXX<span style="color: #8bc34a;">2</span> + publication: PMID<span style="color: #8bc34a;">00001113</span> + submitter_orcid: <span style="color: #B388FF;">[</span>https://orcid.org/<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>,https://orcid.org/<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0001</span>] + additional_submitter_information: Optional free text field for additional information +</pre> +</div> +</div> -<div id="outline-container-org070e13e" class="outline-3"> -<h3 id="org070e13e"><span class="section-number-3">6.1</span> Trouble shooting</h3> +<div id="outline-container-org37fadbc" class="outline-3"> +<h3 id="org37fadbc"><span class="section-number-3">6.1</span> Run the uploader (CLI)</h3> <div class="outline-text-3" id="text-6-1"> <p> -We got an error saying: {"stem": "<a href="http://www.wikidata.org/entity/">http://www.wikidata.org/entity/</a>",… -which means that our location field was not formed correctly! After -fixing it to look like <a href="http://www.wikidata.org/entity/Q65">http://www.wikidata.org/entity/Q65</a> (note http -instead on https and entity instead of wiki) the submission went -through. Reload the page (it won't empty the fields) to re-enable the -submit button. +Installing with pip you should be +able to run +</p> + +<pre class="example"> +bh20sequploader sequence.fasta metadata.yaml +</pre> + + + +<p> +Alternatively the script can be installed from <a href="https://github.com/arvados/bh20-seq-resource#installation">github</a>. Run on the +command line +</p> + +<pre class="example"> +python3 bh20sequploader/main.py example/sequence.fasta example/maximum_metadata_example.yaml +</pre> + + +<p> +after installing dependencies (also described in <a href="https://github.com/arvados/bh20-seq-resource/blob/master/doc/INSTALL.md">INSTALL</a> with the GNU +Guix package manager). +</p> + +<p> +The web interface using this exact same script so it should just work +(TM). +</p> +</div> +</div> + +<div id="outline-container-org39adf09" class="outline-3"> +<h3 id="org39adf09"><span class="section-number-3">6.2</span> Example: uploading bulk GenBank sequences</h3> +<div class="outline-text-3" id="text-6-2"> +<p> +We also use above script to bulk upload GenBank sequences with a <a href="https://github.com/arvados/bh20-seq-resource/blob/master/scripts/from_genbank_to_fasta_and_yaml.py">FASTA +and YAML</a> extractor specific for GenBank. This means that the steps we +took above for uploading a GenBank sequence are already automated. </p> </div> </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 2020-05-30 Sat 10:44</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 2020-05-30 Sat 18:12</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 4dd3078..03f37ab 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -6,26 +6,26 @@ #+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" /> -* Uploading Data -/Work in progress!/ * Table of Contents :TOC:noexport: - [[#uploading-data][Uploading Data]] - - [[#introduction][Introduction]] - [[#step-1-upload-sequence][Step 1: Upload sequence]] - [[#step-2-add-metadata][Step 2: Add metadata]] - [[#obligatory-fields][Obligatory fields]] - [[#optional-fields][Optional fields]] - [[#step-3-submit-to-covid-19-pubseq][Step 3: Submit to COVID-19 PubSeq]] - - [[#step-4-check-output][Step 4: Check output]] - [[#trouble-shooting][Trouble shooting]] + - [[#step-4-check-output][Step 4: Check output]] + - [[#bulk-sequence-uploader][Bulk sequence uploader]] + - [[#run-the-uploader-cli][Run the uploader (CLI)]] + - [[#example-uploading-bulk-genbank-sequences][Example: uploading bulk GenBank sequences]] -* Introduction +* Uploading Data 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. +public resource for global comparisons. A recompute of the pangenome +gets triggered on upload. Read the [[./about][ABOUT]] page for more information. * Step 1: Upload sequence @@ -59,7 +59,7 @@ A number of fields are obligatory: sample id, date, location, technology and authors. The others are optional, but it is valuable to enter them when information is available. Metadata is defined in this [[https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml][schema]]. From this schema we generate the input form. Note that -opitional fields have a question mark in the ~type~. You can add +optional fields have a question mark in the ~type~. You can add metadata yourself, btw, because this is a public resource! See also [[./blog?id=using-covid-19-pubseq-part5][Modify metadata]] for more information. @@ -86,7 +86,7 @@ Estimated collection date. The GenBank page says April 6, 2020. *** Collection location -A search on wikidata says Los Angelos is +A search on wikidata says Los Angeles is https://www.wikidata.org/entity/Q65 *** Sequencing technology @@ -136,12 +136,6 @@ Once you have the sequence and the metadata together, hit the 'Add to Pangenome' button. The data will be checked, submitted and the workflows should kick in! -* Step 4: Check output - -The current pipeline takes 5.5 hours to complete! Once it completes -the updated data can be checked on the [[./download][DOWNLOAD]] page. After completion -of above output this [[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+%22MT536190.1%22+.%0D%0A+++%3Fsample+%3Fp+%3Fo+.%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][SPARQL query]] shows some of the metadata we put -in. ** Trouble shooting @@ -151,3 +145,95 @@ fixing it to look like http://www.wikidata.org/entity/Q65 (note http instead on https and entity instead of wiki) the submission went through. Reload the page (it won't empty the fields) to re-enable the submit button. + + +* Step 4: Check output + +The current pipeline takes 5.5 hours to complete! Once it completes +the updated data can be checked on the [[./download][DOWNLOAD]] page. After completion +of above output this [[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+%22MT536190.1%22+.%0D%0A+++%3Fsample+%3Fp+%3Fo+.%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][SPARQL query]] shows some of the metadata we put +in. + +* Bulk sequence uploader + +Above steps require a manual upload of one sequence with metadata. +What if you have a number of sequences you want to upload in bulk? +For this we have a command line version of the uploader that can +directly submit to COVID-19 PubSeq. It accepts a FASTA sequence +file an associated metadata in [[https://github.com/arvados/bh20-seq-resource/blob/master/example/maximum_metadata_example.yaml][YAML]] format. The YAML matches +the web form and gets validated from the same [[https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml][schema]] looks. The YAML +that you need to create/generate for your samples looks like + +#+begin_src json +id: placeholder + +host: + host_id: XX1 + host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 + host_sex: http://purl.obolibrary.org/obo/PATO_0000384 + host_age: 20 + host_age_unit: http://purl.obolibrary.org/obo/UO_0000036 + host_health_status: http://purl.obolibrary.org/obo/NCIT_C25269 + host_treatment: Process in which the act is intended to modify or alter host status (Compounds) + host_vaccination: [vaccines1,vaccine2] + ethnicity: http://purl.obolibrary.org/obo/HANCESTRO_0010 + additional_host_information: Optional free text field for additional information + +sample: + sample_id: Id of the sample as defined by the submitter + collector_name: Name of the person that took the sample + collecting_institution: Institute that was responsible of sampling + specimen_source: [http://purl.obolibrary.org/obo/NCIT_C155831,http://purl.obolibrary.org/obo/NCIT_C155835] + collection_date: "2020-01-01" + collection_location: http://www.wikidata.org/entity/Q148 + sample_storage_conditions: frozen specimen + source_database_accession: [http://identifiers.org/insdc/LC522350.1#sequence] + additional_collection_information: Optional free text field for additional information + +virus: + virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049 + virus_strain: SARS-CoV-2/human/CHN/HS_8/2020 + +technology: + sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173] + sequence_assembly_method: Protocol used for assembly + sequencing_coverage: [70.0, 100.0] + additional_technology_information: Optional free text field for additional information + +submitter: + authors: [John Doe, Joe Boe, Jonny Oe] + submitter_name: [John Doe] + submitter_address: John Doe's address + originating_lab: John Doe kitchen + lab_address: John Doe's address + provider_sample_id: XXX1 + submitter_sample_id: XXX2 + publication: PMID00001113 + submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001] + additional_submitter_information: Optional free text field for additional information +#+end_src + +** Run the uploader (CLI) + +Installing with pip you should be +able to run + +: bh20sequploader sequence.fasta metadata.yaml + + +Alternatively the script can be installed from [[https://github.com/arvados/bh20-seq-resource#installation][github]]. Run on the +command line + +: python3 bh20sequploader/main.py example/sequence.fasta example/maximum_metadata_example.yaml + +after installing dependencies (also described in [[https://github.com/arvados/bh20-seq-resource/blob/master/doc/INSTALL.md][INSTALL]] with the GNU +Guix package manager). + +The web interface using this exact same script so it should just work +(TM). + +** Example: uploading bulk GenBank sequences + +We also use above script to bulk upload GenBank sequences with a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/from_genbank_to_fasta_and_yaml.py][FASTA +and YAML]] extractor specific for GenBank. This means that the steps we +took above for uploading a GenBank sequence are already automated. diff --git a/doc/blog/using-covid-19-pubseq-part4.html b/doc/blog/using-covid-19-pubseq-part4.html new file mode 100644 index 0000000..67d299e --- /dev/null +++ b/doc/blog/using-covid-19-pubseq-part4.html @@ -0,0 +1,266 @@ +<?xml version="1.0" encoding="utf-8"?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" +"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> +<head> +<!-- 2020-05-30 Sat 11:52 --> +<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> +<meta name="viewport" content="width=device-width, initial-scale=1" /> +<title>‎</title> +<meta name="generator" content="Org mode" /> +<meta name="author" content="Pjotr Prins" /> +<style type="text/css"> + <!--/*--><![CDATA[/*><!--*/ + .title { text-align: center; + margin-bottom: .2em; } + .subtitle { text-align: center; + font-size: medium; + font-weight: bold; + margin-top:0; } + .todo { font-family: monospace; color: red; } + .done { font-family: monospace; color: green; } + .priority { font-family: monospace; color: orange; } + .tag { background-color: #eee; font-family: monospace; + padding: 2px; font-size: 80%; font-weight: normal; } + .timestamp { color: #bebebe; } + .timestamp-kwd { color: #5f9ea0; } + .org-right { margin-left: auto; margin-right: 0px; text-align: right; } + .org-left { margin-left: 0px; margin-right: auto; text-align: left; } + .org-center { margin-left: auto; margin-right: auto; text-align: center; } + .underline { text-decoration: underline; } + #postamble p, #preamble p { font-size: 90%; margin: .2em; } + p.verse { margin-left: 3%; } + pre { + border: 1px solid #ccc; + box-shadow: 3px 3px 3px #eee; + padding: 8pt; + font-family: monospace; + overflow: auto; + margin: 1.2em; + } + pre.src { + position: relative; + overflow: visible; + padding-top: 1.2em; + } + pre.src:before { + display: none; + position: absolute; + background-color: white; + top: -10px; + right: 10px; + padding: 3px; + border: 1px solid black; + } + pre.src:hover:before { display: inline;} + /* Languages per Org manual */ + pre.src-asymptote:before { content: 'Asymptote'; } + pre.src-awk:before { content: 'Awk'; } + pre.src-C:before { content: 'C'; } + /* pre.src-C++ doesn't work in CSS */ + pre.src-clojure:before { content: 'Clojure'; } + pre.src-css:before { content: 'CSS'; } + pre.src-D:before { content: 'D'; } + pre.src-ditaa:before { content: 'ditaa'; } + pre.src-dot:before { content: 'Graphviz'; } + pre.src-calc:before { content: 'Emacs Calc'; } + pre.src-emacs-lisp:before { content: 'Emacs Lisp'; } + pre.src-fortran:before { content: 'Fortran'; } + pre.src-gnuplot:before { content: 'gnuplot'; } + pre.src-haskell:before { content: 'Haskell'; } + pre.src-hledger:before { content: 'hledger'; } + pre.src-java:before { content: 'Java'; } + pre.src-js:before { content: 'Javascript'; } + pre.src-latex:before { content: 'LaTeX'; } + pre.src-ledger:before { content: 'Ledger'; } + pre.src-lisp:before { content: 'Lisp'; } + pre.src-lilypond:before { content: 'Lilypond'; } + pre.src-lua:before { content: 'Lua'; } + pre.src-matlab:before { content: 'MATLAB'; } + pre.src-mscgen:before { content: 'Mscgen'; } + pre.src-ocaml:before { content: 'Objective Caml'; } + pre.src-octave:before { content: 'Octave'; } + pre.src-org:before { content: 'Org mode'; } + pre.src-oz:before { content: 'OZ'; } + pre.src-plantuml:before { content: 'Plantuml'; } + pre.src-processing:before { content: 'Processing.js'; } + pre.src-python:before { content: 'Python'; } + pre.src-R:before { content: 'R'; } + pre.src-ruby:before { content: 'Ruby'; } + pre.src-sass:before { content: 'Sass'; } + pre.src-scheme:before { content: 'Scheme'; } + pre.src-screen:before { content: 'Gnu Screen'; } + pre.src-sed:before { content: 'Sed'; } + pre.src-sh:before { content: 'shell'; } + pre.src-sql:before { content: 'SQL'; } + pre.src-sqlite:before { content: 'SQLite'; } + /* additional languages in org.el's org-babel-load-languages alist */ + pre.src-forth:before { content: 'Forth'; } + pre.src-io:before { content: 'IO'; } + pre.src-J:before { content: 'J'; } + pre.src-makefile:before { content: 'Makefile'; } + pre.src-maxima:before { content: 'Maxima'; } + pre.src-perl:before { content: 'Perl'; } + pre.src-picolisp:before { content: 'Pico Lisp'; } + pre.src-scala:before { content: 'Scala'; } + pre.src-shell:before { content: 'Shell Script'; } + pre.src-ebnf2ps:before { content: 'ebfn2ps'; } + /* additional language identifiers per "defun org-babel-execute" + in ob-*.el */ + pre.src-cpp:before { content: 'C++'; } + pre.src-abc:before { content: 'ABC'; } + pre.src-coq:before { content: 'Coq'; } + pre.src-groovy:before { content: 'Groovy'; } + /* additional language identifiers from org-babel-shell-names in + ob-shell.el: ob-shell is the only babel language using a lambda to put + the execution function name together. */ + pre.src-bash:before { content: 'bash'; } + pre.src-csh:before { content: 'csh'; } + pre.src-ash:before { content: 'ash'; } + pre.src-dash:before { content: 'dash'; } + pre.src-ksh:before { content: 'ksh'; } + pre.src-mksh:before { content: 'mksh'; } + pre.src-posh:before { content: 'posh'; } + /* Additional Emacs modes also supported by the LaTeX listings package */ + pre.src-ada:before { content: 'Ada'; } + pre.src-asm:before { content: 'Assembler'; } + pre.src-caml:before { content: 'Caml'; } + pre.src-delphi:before { content: 'Delphi'; } + pre.src-html:before { content: 'HTML'; } + pre.src-idl:before { content: 'IDL'; } + pre.src-mercury:before { content: 'Mercury'; } + pre.src-metapost:before { content: 'MetaPost'; } + pre.src-modula-2:before { content: 'Modula-2'; } + pre.src-pascal:before { content: 'Pascal'; } + pre.src-ps:before { content: 'PostScript'; } + pre.src-prolog:before { content: 'Prolog'; } + pre.src-simula:before { content: 'Simula'; } + pre.src-tcl:before { content: 'tcl'; } + pre.src-tex:before { content: 'TeX'; } + pre.src-plain-tex:before { content: 'Plain TeX'; } + pre.src-verilog:before { content: 'Verilog'; } + pre.src-vhdl:before { content: 'VHDL'; } + pre.src-xml:before { content: 'XML'; } + pre.src-nxml:before { content: 'XML'; } + /* add a generic configuration mode; LaTeX export needs an additional + (add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */ + pre.src-conf:before { content: 'Configuration File'; } + + table { border-collapse:collapse; } + caption.t-above { caption-side: top; } + caption.t-bottom { caption-side: bottom; } + td, th { vertical-align:top; } + th.org-right { text-align: center; } + th.org-left { text-align: center; } + th.org-center { text-align: center; } + td.org-right { text-align: right; } + td.org-left { text-align: left; } + td.org-center { text-align: center; } + dt { font-weight: bold; } + .footpara { display: inline; } + .footdef { margin-bottom: 1em; } + .figure { padding: 1em; } + .figure p { text-align: center; } + .equation-container { + display: table; + text-align: center; + width: 100%; + } + .equation { + vertical-align: middle; + } + .equation-label { + display: table-cell; + text-align: right; + vertical-align: middle; + } + .inlinetask { + padding: 10px; + border: 2px solid gray; + margin: 10px; + background: #ffffcc; + } + #org-div-home-and-up + { text-align: right; font-size: 70%; white-space: nowrap; } + textarea { overflow-x: auto; } + .linenr { font-size: smaller } + .code-highlighted { background-color: #ffff00; } + .org-info-js_info-navigation { border-style: none; } + #org-info-js_console-label + { font-size: 10px; font-weight: bold; white-space: nowrap; } + .org-info-js_search-highlight + { background-color: #ffff00; color: #000000; font-weight: bold; } + .org-svg { width: 90%; } + /*]]>*/--> +</style> +<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. +*/ +<!--/*--><![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; + } +/*]]>*///--> +</script> +</head> +<body> +<div id="content"> +<div id="table-of-contents"> +<h2>Table of Contents</h2> +<div id="text-table-of-contents"> +<ul> +<li><a href="#orgda6f48c">1. Modify Workflow</a></li> +</ul> +</div> +</div> +<div id="outline-container-orgda6f48c" class="outline-2"> +<h2 id="orgda6f48c"><span class="section-number-2">1</span> Modify Workflow</h2> +<div class="outline-text-2" id="text-1"> +<p> +<i>Work in progress!</i> +</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 2020-05-30 Sat 11:52</small>. +</div> +</body> +</html> diff --git a/doc/blog/using-covid-19-pubseq-part4.org b/doc/blog/using-covid-19-pubseq-part4.org index c147ba3..58a1f56 100644 --- a/doc/blog/using-covid-19-pubseq-part4.org +++ b/doc/blog/using-covid-19-pubseq-part4.org @@ -1,2 +1,3 @@ -/Work in progress!/ +* Modify Workflow +/Work in progress!/ diff --git a/doc/blog/using-covid-19-pubseq-part5.html b/doc/blog/using-covid-19-pubseq-part5.html new file mode 100644 index 0000000..30a3f83 --- /dev/null +++ b/doc/blog/using-covid-19-pubseq-part5.html @@ -0,0 +1,277 @@ +<?xml version="1.0" encoding="utf-8"?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" +"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> +<head> +<!-- 2020-05-30 Sat 11:59 --> +<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> +<meta name="viewport" content="width=device-width, initial-scale=1" /> +<title>‎</title> +<meta name="generator" content="Org mode" /> +<meta name="author" content="Pjotr Prins" /> +<style type="text/css"> + <!--/*--><![CDATA[/*><!--*/ + .title { text-align: center; + margin-bottom: .2em; } + .subtitle { text-align: center; + font-size: medium; + font-weight: bold; + margin-top:0; } + .todo { font-family: monospace; color: red; } + .done { font-family: monospace; color: green; } + .priority { font-family: monospace; color: orange; } + .tag { background-color: #eee; font-family: monospace; + padding: 2px; font-size: 80%; font-weight: normal; } + .timestamp { color: #bebebe; } + .timestamp-kwd { color: #5f9ea0; } + .org-right { margin-left: auto; margin-right: 0px; text-align: right; } + .org-left { margin-left: 0px; margin-right: auto; text-align: left; } + .org-center { margin-left: auto; margin-right: auto; text-align: center; } + .underline { text-decoration: underline; } + #postamble p, #preamble p { font-size: 90%; margin: .2em; } + p.verse { margin-left: 3%; } + pre { + border: 1px solid #ccc; + box-shadow: 3px 3px 3px #eee; + padding: 8pt; + font-family: monospace; + overflow: auto; + margin: 1.2em; + } + pre.src { + position: relative; + overflow: visible; + padding-top: 1.2em; + } + pre.src:before { + display: none; + position: absolute; + background-color: white; + top: -10px; + right: 10px; + padding: 3px; + border: 1px solid black; + } + pre.src:hover:before { display: inline;} + /* Languages per Org manual */ + pre.src-asymptote:before { content: 'Asymptote'; } + pre.src-awk:before { content: 'Awk'; } + pre.src-C:before { content: 'C'; } + /* pre.src-C++ doesn't work in CSS */ + pre.src-clojure:before { content: 'Clojure'; } + pre.src-css:before { content: 'CSS'; } + pre.src-D:before { content: 'D'; } + pre.src-ditaa:before { content: 'ditaa'; } + pre.src-dot:before { content: 'Graphviz'; } + pre.src-calc:before { content: 'Emacs Calc'; } + pre.src-emacs-lisp:before { content: 'Emacs Lisp'; } + pre.src-fortran:before { content: 'Fortran'; } + pre.src-gnuplot:before { content: 'gnuplot'; } + pre.src-haskell:before { content: 'Haskell'; } + pre.src-hledger:before { content: 'hledger'; } + pre.src-java:before { content: 'Java'; } + pre.src-js:before { content: 'Javascript'; } + pre.src-latex:before { content: 'LaTeX'; } + pre.src-ledger:before { content: 'Ledger'; } + pre.src-lisp:before { content: 'Lisp'; } + pre.src-lilypond:before { content: 'Lilypond'; } + pre.src-lua:before { content: 'Lua'; } + pre.src-matlab:before { content: 'MATLAB'; } + pre.src-mscgen:before { content: 'Mscgen'; } + pre.src-ocaml:before { content: 'Objective Caml'; } + pre.src-octave:before { content: 'Octave'; } + pre.src-org:before { content: 'Org mode'; } + pre.src-oz:before { content: 'OZ'; } + pre.src-plantuml:before { content: 'Plantuml'; } + pre.src-processing:before { content: 'Processing.js'; } + pre.src-python:before { content: 'Python'; } + pre.src-R:before { content: 'R'; } + pre.src-ruby:before { content: 'Ruby'; } + pre.src-sass:before { content: 'Sass'; } + pre.src-scheme:before { content: 'Scheme'; } + pre.src-screen:before { content: 'Gnu Screen'; } + pre.src-sed:before { content: 'Sed'; } + pre.src-sh:before { content: 'shell'; } + pre.src-sql:before { content: 'SQL'; } + pre.src-sqlite:before { content: 'SQLite'; } + /* additional languages in org.el's org-babel-load-languages alist */ + pre.src-forth:before { content: 'Forth'; } + pre.src-io:before { content: 'IO'; } + pre.src-J:before { content: 'J'; } + pre.src-makefile:before { content: 'Makefile'; } + pre.src-maxima:before { content: 'Maxima'; } + pre.src-perl:before { content: 'Perl'; } + pre.src-picolisp:before { content: 'Pico Lisp'; } + pre.src-scala:before { content: 'Scala'; } + pre.src-shell:before { content: 'Shell Script'; } + pre.src-ebnf2ps:before { content: 'ebfn2ps'; } + /* additional language identifiers per "defun org-babel-execute" + in ob-*.el */ + pre.src-cpp:before { content: 'C++'; } + pre.src-abc:before { content: 'ABC'; } + pre.src-coq:before { content: 'Coq'; } + pre.src-groovy:before { content: 'Groovy'; } + /* additional language identifiers from org-babel-shell-names in + ob-shell.el: ob-shell is the only babel language using a lambda to put + the execution function name together. */ + pre.src-bash:before { content: 'bash'; } + pre.src-csh:before { content: 'csh'; } + pre.src-ash:before { content: 'ash'; } + pre.src-dash:before { content: 'dash'; } + pre.src-ksh:before { content: 'ksh'; } + pre.src-mksh:before { content: 'mksh'; } + pre.src-posh:before { content: 'posh'; } + /* Additional Emacs modes also supported by the LaTeX listings package */ + pre.src-ada:before { content: 'Ada'; } + pre.src-asm:before { content: 'Assembler'; } + pre.src-caml:before { content: 'Caml'; } + pre.src-delphi:before { content: 'Delphi'; } + pre.src-html:before { content: 'HTML'; } + pre.src-idl:before { content: 'IDL'; } + pre.src-mercury:before { content: 'Mercury'; } + pre.src-metapost:before { content: 'MetaPost'; } + pre.src-modula-2:before { content: 'Modula-2'; } + pre.src-pascal:before { content: 'Pascal'; } + pre.src-ps:before { content: 'PostScript'; } + pre.src-prolog:before { content: 'Prolog'; } + pre.src-simula:before { content: 'Simula'; } + pre.src-tcl:before { content: 'tcl'; } + pre.src-tex:before { content: 'TeX'; } + pre.src-plain-tex:before { content: 'Plain TeX'; } + pre.src-verilog:before { content: 'Verilog'; } + pre.src-vhdl:before { content: 'VHDL'; } + pre.src-xml:before { content: 'XML'; } + pre.src-nxml:before { content: 'XML'; } + /* add a generic configuration mode; LaTeX export needs an additional + (add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */ + pre.src-conf:before { content: 'Configuration File'; } + + table { border-collapse:collapse; } + caption.t-above { caption-side: top; } + caption.t-bottom { caption-side: bottom; } + td, th { vertical-align:top; } + th.org-right { text-align: center; } + th.org-left { text-align: center; } + th.org-center { text-align: center; } + td.org-right { text-align: right; } + td.org-left { text-align: left; } + td.org-center { text-align: center; } + dt { font-weight: bold; } + .footpara { display: inline; } + .footdef { margin-bottom: 1em; } + .figure { padding: 1em; } + .figure p { text-align: center; } + .equation-container { + display: table; + text-align: center; + width: 100%; + } + .equation { + vertical-align: middle; + } + .equation-label { + display: table-cell; + text-align: right; + vertical-align: middle; + } + .inlinetask { + padding: 10px; + border: 2px solid gray; + margin: 10px; + background: #ffffcc; + } + #org-div-home-and-up + { text-align: right; font-size: 70%; white-space: nowrap; } + textarea { overflow-x: auto; } + .linenr { font-size: smaller } + .code-highlighted { background-color: #ffff00; } + .org-info-js_info-navigation { border-style: none; } + #org-info-js_console-label + { font-size: 10px; font-weight: bold; white-space: nowrap; } + .org-info-js_search-highlight + { background-color: #ffff00; color: #000000; font-weight: bold; } + .org-svg { width: 90%; } + /*]]>*/--> +</style> +<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. +*/ +<!--/*--><![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; + } +/*]]>*///--> +</script> +</head> +<body> +<div id="content"> +<div id="table-of-contents"> +<h2>Table of Contents</h2> +<div id="text-table-of-contents"> +<ul> +<li><a href="#org31c224e">1. Modify Metadata</a></li> +</ul> +</div> +</div> +<div id="outline-container-org31c224e" class="outline-2"> +<h2 id="org31c224e"><span class="section-number-2">1</span> Modify Metadata</h2> +<div class="outline-text-2" id="text-1"> +<p> +The public sequence resource uses multiple data formats listed on the +<a href="./download">DOWNLOAD</a> page. One of the most exciting features is the full support +for RDF and semantic web/linked data ontologies. This technology +allows for querying data in unprescribed ways - that is, you can +formulate your own queries without dealing with a preset model of that +data (so typical of CSV files and SQL tables). Examples of exploring +data are listed <a href="./blog?id=using-covid-19-pubseq-part1">here</a>. +</p> + +<p> +In this BLOG we are going to look at the metadata entered on the +<a href="./">COVID-19 PubSeq</a> website (or command line client). +</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 2020-05-30 Sat 11:59</small>. +</div> +</body> +</html> diff --git a/doc/blog/using-covid-19-pubseq-part5.org b/doc/blog/using-covid-19-pubseq-part5.org index c147ba3..8d7504e 100644 --- a/doc/blog/using-covid-19-pubseq-part5.org +++ b/doc/blog/using-covid-19-pubseq-part5.org @@ -1,2 +1,17 @@ -/Work in progress!/ +* Modify Metadata +The public sequence resource uses multiple data formats listed on the +[[./download][DOWNLOAD]] page. One of the most exciting features is the full support +for RDF and semantic web/linked data ontologies. This technology +allows for querying data in unprescribed ways - that is, you can +formulate your own queries without dealing with a preset model of that +data (so typical of CSV files and SQL tables). Examples of exploring +data are listed [[./blog?id=using-covid-19-pubseq-part1][here]]. + +In this BLOG we are going to look at the metadata entered on the +[[./][COVID-19 PubSeq]] website (or command line client). It is important to +understand that you and us can change that information. + +* What is the schema? + +* How is the website generated? |