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authorPjotr Prins2020-07-17 11:06:33 +0100
committerPjotr Prins2020-07-17 11:06:33 +0100
commitc69046ee9a5e24eadcd8cb885633328b0fd88011 (patch)
tree0b05483fa8d971ea01fe03113dcd198167b6b7d8 /doc
parent48caca541bf19e1c4f75f5b95272b99eb06a02bc (diff)
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Update generated docs
Diffstat (limited to 'doc')
-rw-r--r--doc/blog/using-covid-19-pubseq-part1.html192
-rw-r--r--doc/blog/using-covid-19-pubseq-part4.html44
-rw-r--r--doc/blog/using-covid-19-pubseq-part5.html194
3 files changed, 305 insertions, 125 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part1.html b/doc/blog/using-covid-19-pubseq-part1.html
index 1959fac..0e6136c 100644
--- a/doc/blog/using-covid-19-pubseq-part1.html
+++ b/doc/blog/using-covid-19-pubseq-part1.html
@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
-<!-- 2020-05-29 Fri 12:06 -->
+<!-- 2020-07-17 Fri 05:05 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>COVID-19 PubSeq (part 1)</title>
@@ -248,20 +248,20 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
-<li><a href="#org9afe6ab">1. What does this mean?</a></li>
-<li><a href="#orgf4bc3d4">2. Fetch sequence data</a></li>
-<li><a href="#org9d7d482">3. Predicates</a></li>
-<li><a href="#orgc6046bb">4. Fetch submitter info and other metadata</a></li>
-<li><a href="#orgdcb216b">5. Fetch all sequences from Washington state</a></li>
-<li><a href="#org7060f51">6. Discussion</a></li>
-<li><a href="#orgdc51ccc">7. Acknowledgements</a></li>
+<li><a href="#org0db5db0">1. What does this mean?</a></li>
+<li><a href="#orge5267fd">2. Fetch sequence data</a></li>
+<li><a href="#orgfbd3adc">3. Predicates</a></li>
+<li><a href="#org08e70e1">4. Fetch submitter info and other metadata</a></li>
+<li><a href="#org9194557">5. Fetch all sequences from Washington state</a></li>
+<li><a href="#org76317ad">6. Discussion</a></li>
+<li><a href="#orgeb871a1">7. Acknowledgements</a></li>
</ul>
</div>
</div>
-<div id="outline-container-org9afe6ab" class="outline-2">
-<h2 id="org9afe6ab"><span class="section-number-2">1</span> What does this mean?</h2>
+<div id="outline-container-org0db5db0" class="outline-2">
+<h2 id="org0db5db0"><span class="section-number-2">1</span> What does this mean?</h2>
<div class="outline-text-2" id="text-1">
<p>
This means that when someone uploads a SARS-CoV-2 sequence using one
@@ -274,24 +274,24 @@ expressed in a <a href="https://github.com/arvados/bh20-seq-resource/blob/master
type: record
fields:
host_species:
- doc: Host species as defined in NCBITaxon, e.g. http://purl.obolibrary.org/obo/NCBITaxon_<span style="color: #8bc34a;">9606</span> for Homo sapiens
+ doc: Host species as defined in NCBITaxon, e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens
type: string
jsonldPredicate:
- _id: http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0000532</span>
- _type: <span style="color: #9ccc65;">"@id"</span>
- noLinkCheck: <span style="color: #8bc34a;">true</span>
+ _id: http://www.ebi.ac.uk/efo/EFO_0000532
+ _type: "@id"
+ noLinkCheck: true
host_sex:
- doc: Sex of the host as defined in PATO, expect male <span style="color: #e91e63;">()</span> or female <span style="color: #e91e63;">()</span>
+ doc: Sex of the host as defined in PATO, expect male () or female ()
type: string?
jsonldPredicate:
- _id: http://purl.obolibrary.org/obo/PATO_<span style="color: #8bc34a;">0000047</span>
- _type: <span style="color: #9ccc65;">"@id"</span>
- noLinkCheck: <span style="color: #8bc34a;">true</span>
+ _id: http://purl.obolibrary.org/obo/PATO_0000047
+ _type: "@id"
+ noLinkCheck: true
host_age:
- doc: Age of the host as number <span style="color: #e91e63;">(</span>e.g. <span style="color: #8bc34a;">50</span><span style="color: #e91e63;">)</span>
+ doc: Age of the host as number (e.g. 50)
type: int?
jsonldPredicate:
- _id: http://purl.obolibrary.org/obo/PATO_<span style="color: #8bc34a;">0000011</span>
+ _id: http://purl.obolibrary.org/obo/PATO_0000011
</pre>
</div>
@@ -314,8 +314,8 @@ initiative!
</div>
-<div id="outline-container-orgf4bc3d4" class="outline-2">
-<h2 id="orgf4bc3d4"><span class="section-number-2">2</span> Fetch sequence data</h2>
+<div id="outline-container-orge5267fd" class="outline-2">
+<h2 id="orge5267fd"><span class="section-number-2">2</span> Fetch sequence data</h2>
<div class="outline-text-2" id="text-2">
<p>
The latest run of the pipeline can be viewed <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">here</a>. Each of these
@@ -339,8 +339,8 @@ these identifiers throughout.
</div>
</div>
-<div id="outline-container-org9d7d482" class="outline-2">
-<h2 id="org9d7d482"><span class="section-number-2">3</span> Predicates</h2>
+<div id="outline-container-orgfbd3adc" class="outline-2">
+<h2 id="orgfbd3adc"><span class="section-number-2">3</span> Predicates</h2>
<div class="outline-text-2" id="text-3">
<p>
To explore an RDF dataset, the first query we can do is open and gets
@@ -350,10 +350,10 @@ the following in a SPARQL end point
</p>
<div class="org-src-container">
-<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?p
-<span style="color: #e91e63;">{</span>
+<pre class="src src-sql">select distinct ?p
+{
?o ?p ?s
-<span style="color: #e91e63;">}</span>
+}
</pre>
</div>
@@ -364,10 +364,10 @@ To get a <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&amp;q
</p>
<div class="org-src-container">
-<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?g
-<span style="color: #e91e63;">{</span>
- GRAPH ?g <span style="color: #2196F3;">{</span>?s ?p ?o<span style="color: #2196F3;">}</span>
-<span style="color: #e91e63;">}</span>
+<pre class="src src-sql">select distinct ?g
+{
+ GRAPH ?g {?s ?p ?o}
+}
</pre>
</div>
@@ -383,10 +383,10 @@ To list all submitters, try
</p>
<div class="org-src-container">
-<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?s
-<span style="color: #e91e63;">{</span>
- ?o <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">#MainSchema/submitter&gt;</a> ?s
-<span style="color: #e91e63;">}</span>
+<pre class="src src-sql">select distinct ?s
+{
+ ?o &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/submitter&gt; ?s
+}
</pre>
</div>
@@ -397,11 +397,11 @@ and by
</p>
<div class="org-src-container">
-<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?s
-<span style="color: #e91e63;">{</span>
- ?o <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">#MainSchema/submitter&gt;</a> ?id .
+<pre class="src src-sql">select distinct ?s
+{
+ ?o &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/submitter&gt; ?id .
?id ?p ?s
-<span style="color: #e91e63;">}</span>
+}
</pre>
</div>
@@ -415,12 +415,12 @@ To lift the full URL out of the query you can use a header like
</p>
<div class="org-src-container">
-<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
-<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?submitter
-<span style="color: #e91e63;">{</span>
+<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+select distinct ?dataset ?submitter
+{
?dataset pubseq:submitter ?id .
?id ?p ?submitter
-<span style="color: #e91e63;">}</span>
+}
</pre>
</div>
@@ -438,32 +438,32 @@ Now we got this far, lets <a href="http://sparql.genenetwork.org/sparql/?default
</p>
<div class="org-src-container">
-<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
-<span style="color: #fff59d;">select</span> <span style="color: #e91e63;">(</span><span style="color: #ff8A65;">COUNT</span><span style="color: #2196F3;">(</span><span style="color: #fff59d;">distinct</span> ?dataset<span style="color: #2196F3;">)</span> <span style="color: #fff59d;">as</span> ?num<span style="color: #e91e63;">)</span>
-<span style="color: #e91e63;">{</span>
+<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+select (COUNT(distinct ?dataset) as ?num)
+{
?dataset pubseq:submitter ?id .
?id ?p ?submitter
-<span style="color: #e91e63;">}</span>
+}
</pre>
</div>
</div>
</div>
-<div id="outline-container-orgc6046bb" class="outline-2">
-<h2 id="orgc6046bb"><span class="section-number-2">4</span> Fetch submitter info and other metadata</h2>
+<div id="outline-container-org08e70e1" class="outline-2">
+<h2 id="org08e70e1"><span class="section-number-2">4</span> Fetch submitter info and other metadata</h2>
<div class="outline-text-2" id="text-4">
<p>
To get dataests with submitters we can do the above
</p>
<div class="org-src-container">
-<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
-<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?p ?submitter
-<span style="color: #e91e63;">{</span>
+<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+select distinct ?dataset ?p ?submitter
+{
?dataset pubseq:submitter ?id .
?id ?p ?submitter
-<span style="color: #e91e63;">}</span>
+}
</pre>
</div>
@@ -480,13 +480,13 @@ Let's focus on one sample with
</p>
<div class="org-src-container">
-<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
-<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?submitter
-<span style="color: #e91e63;">{</span>
+<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+select distinct ?dataset ?submitter
+{
?dataset pubseq:submitter ?id .
?id ?p ?submitter .
- FILTER<span style="color: #2196F3;">(</span><span style="color: #fff59d;">CONTAINS</span><span style="color: #EF6C00;">(</span>?submitter,"Roychoudhury"<span style="color: #EF6C00;">)</span><span style="color: #2196F3;">)</span> .
-<span style="color: #e91e63;">}</span>
+ FILTER(CONTAINS(?submitter,"Roychoudhury")) .
+}
</pre>
</div>
@@ -496,12 +496,12 @@ see if we can get a sample ID by listing sample predicates
</p>
<div class="org-src-container">
-<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
-<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?p
-<span style="color: #e91e63;">{</span>
+<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+select distinct ?p
+{
?dataset ?p ?o .
?dataset pubseq:submitter ?id .
-<span style="color: #e91e63;">}</span>
+}
</pre>
</div>
@@ -513,15 +513,15 @@ Let's zoom in on those of Roychoudhury with
<div class="org-src-container">
-<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/&gt;</a>
-<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?sid ?sample ?p1 ?dataset ?submitter
-<span style="color: #e91e63;">{</span>
+<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+select distinct ?sid ?sample ?p1 ?dataset ?submitter
+{
?dataset pubseq:submitter ?id .
?id ?p ?submitter .
- FILTER<span style="color: #2196F3;">(</span><span style="color: #fff59d;">CONTAINS</span><span style="color: #EF6C00;">(</span>?submitter,"Roychoudhury"<span style="color: #EF6C00;">)</span><span style="color: #2196F3;">)</span> .
+ FILTER(CONTAINS(?submitter,"Roychoudhury")) .
?dataset pubseq:sample ?sid .
?sid ?p1 ?sample
-<span style="color: #e91e63;">}</span>
+}
</pre>
</div>
@@ -532,18 +532,13 @@ this database. Let's focus on one sample "MT326090.1" with predicate
</p>
<div class="org-src-container">
-<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
-PREFIX sio: &lt;http://semanticscience.org/resource/">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
-PREFIX sio: &lt;http://semanticscience.org/resource/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
-PREFIX sio: &lt;http://semanticscience.org/resource/">#MainSchema/&gt;
-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
-PREFIX sio: &lt;http://semanticscience.org/resource/">PREFIX</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
-PREFIX sio: &lt;http://semanticscience.org/resource/"> sio: &lt;http://semanticscience.org/resource/&gt;</a>
-<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?sample ?p ?o
-<span style="color: #e91e63;">{</span>
+<pre class="src src-sql">PREFIX pubseq: &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/&gt;
+PREFIX sio: &lt;http://semanticscience.org/resource/&gt;
+select distinct ?sample ?p ?o
+{
?sample sio:SIO_000115 "MT326090.1" .
?sample ?p ?o .
-<span style="color: #e91e63;">}</span>
+}
</pre>
</div>
@@ -561,8 +556,8 @@ to view/query the database.
</div>
</div>
-<div id="outline-container-orgdcb216b" class="outline-2">
-<h2 id="orgdcb216b"><span class="section-number-2">5</span> Fetch all sequences from Washington state</h2>
+<div id="outline-container-org9194557" class="outline-2">
+<h2 id="org9194557"><span class="section-number-2">5</span> Fetch all sequences from Washington state</h2>
<div class="outline-text-2" id="text-5">
<p>
Now we know how to get at the origin we can do it the other way round
@@ -570,15 +565,11 @@ and fetch all sequences referring to Washington state
</p>
<div class="org-src-container">
-<pre class="src src-sql">
-<span style="color: #fff59d;">select</span> ?seq ?sample
-<span style="color: #e91e63;">{</span>
- ?seq <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
- ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223">&lt;http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
- ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
- ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223">#MainSchema/sample&gt; ?sample .
- ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223&gt;</a>
-<span style="color: #e91e63;">}</span>
+<pre class="src src-sql">select ?seq ?sample
+{
+ ?seq &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q1223&gt;
+}
</pre>
</div>
@@ -586,11 +577,26 @@ and fetch all sequences referring to Washington state
which lists 300 sequences originating from Washington state! Which is almost
half of the set coming out of GenBank.
</p>
+
+<p>
+Likewise to list all sequences from Turkey we can find the wikidata
+entity is <a href="https://www.wikidata.org/wiki/Q43">Q43</a>:
+</p>
+
+<div class="org-src-container">
+<pre class="src src-sql">select ?seq ?sample
+{
+ ?seq &lt;http://biohackathon.org/bh20-seq-schema#MainSchema/sample&gt; ?sample .
+ ?sample &lt;http://purl.obolibrary.org/obo/GAZ_00000448&gt; &lt;http://www.wikidata.org/entity/Q43&gt;
+}
+</pre>
</div>
</div>
+</div>
+
-<div id="outline-container-org7060f51" class="outline-2">
-<h2 id="org7060f51"><span class="section-number-2">6</span> Discussion</h2>
+<div id="outline-container-org76317ad" class="outline-2">
+<h2 id="org76317ad"><span class="section-number-2">6</span> Discussion</h2>
<div class="outline-text-2" id="text-6">
<p>
The public sequence uploader collects sequences, raw data and
@@ -601,8 +607,8 @@ referenced in publications and origins are citeable.
</div>
</div>
-<div id="outline-container-orgdc51ccc" class="outline-2">
-<h2 id="orgdc51ccc"><span class="section-number-2">7</span> Acknowledgements</h2>
+<div id="outline-container-orgeb871a1" class="outline-2">
+<h2 id="orgeb871a1"><span class="section-number-2">7</span> Acknowledgements</h2>
<div class="outline-text-2" id="text-7">
<p>
The overall effort was due to magnificent freely donated input by a
@@ -617,7 +623,7 @@ Garrison this initiative would not have existed!
</div>
</div>
<div id="postamble" class="status">
-<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-29 Fri 12:06</small>.
+<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-17 Fri 05:02</small>.
</div>
</body>
</html>
diff --git a/doc/blog/using-covid-19-pubseq-part4.html b/doc/blog/using-covid-19-pubseq-part4.html
index b5a05ca..c975c21 100644
--- a/doc/blog/using-covid-19-pubseq-part4.html
+++ b/doc/blog/using-covid-19-pubseq-part4.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>
-<!-- 2020-07-12 Sun 06:24 -->
+<!-- 2020-07-17 Fri 05:04 -->
<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 4)</title>
@@ -161,6 +161,19 @@
.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;
@@ -186,7 +199,7 @@
@licstart The following is the entire license notice for the
JavaScript code in this tag.
-Copyright (C) 2012-2018 Free Software Foundation, Inc.
+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
@@ -235,15 +248,16 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
-<li><a href="#org8f8b64a">1. What does this mean?</a></li>
-<li><a href="#orgcc7a403">2. Modify Workflow</a></li>
+<li><a href="#orgc2ee09f">1. What does this mean?</a></li>
+<li><a href="#org0d37881">2. Where can I find the workflows?</a></li>
+<li><a href="#orgddb0531">3. Modify Workflow</a></li>
</ul>
</div>
</div>
-<div id="outline-container-org8f8b64a" class="outline-2">
-<h2 id="org8f8b64a"><span class="section-number-2">1</span> What does this mean?</h2>
+<div id="outline-container-orgc2ee09f" class="outline-2">
+<h2 id="orgc2ee09f"><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
@@ -253,18 +267,28 @@ which triggers a rerun of our workflows.
</div>
</div>
-
-<div id="outline-container-orgcc7a403" class="outline-2">
-<h2 id="orgcc7a403"><span class="section-number-2">2</span> Modify Workflow</h2>
+<div id="outline-container-org0d37881" class="outline-2">
+<h2 id="org0d37881"><span class="section-number-2">2</span> Where can I find the workflows?</h2>
<div class="outline-text-2" id="text-2">
<p>
+Workflows are written in the common workflow language (CWL) and listed
+on <a href="https://github.com/arvados/bh20-seq-resource/tree/master/workflows">github</a>. PubSeq being an open project these workflows can be studied
+and modified!
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgddb0531" class="outline-2">
+<h2 id="orgddb0531"><span class="section-number-2">3</span> Modify Workflow</h2>
+<div class="outline-text-2" id="text-3">
+<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 2020-07-12 Sun 06:24</small>.
+<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-17 Fri 01:47</small>.
</div>
</body>
</html>
diff --git a/doc/blog/using-covid-19-pubseq-part5.html b/doc/blog/using-covid-19-pubseq-part5.html
index 80bf559..4caa5ac 100644
--- a/doc/blog/using-covid-19-pubseq-part5.html
+++ b/doc/blog/using-covid-19-pubseq-part5.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>
-<!-- 2020-07-12 Sun 06:24 -->
+<!-- 2020-07-17 Fri 05:03 -->
<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 4)</title>
@@ -161,6 +161,19 @@
.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;
@@ -186,7 +199,7 @@
@licstart The following is the entire license notice for the
JavaScript code in this tag.
-Copyright (C) 2012-2018 Free Software Foundation, Inc.
+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
@@ -235,38 +248,40 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
-<li><a href="#org871ad58">1. Modify Metadata</a></li>
-<li><a href="#org07e8755">2. What is the schema?</a></li>
-<li><a href="#org4857280">3. How is the website generated?</a></li>
-<li><a href="#orge709ae2">4. Modifying the schema</a></li>
+<li><a href="#org758b923">1. Modify Metadata</a></li>
+<li><a href="#orgec32c13">2. What is the schema?</a></li>
+<li><a href="#org2e487b2">3. How is the website generated?</a></li>
+<li><a href="#orge4dfe84">4. Modifying the schema</a></li>
+<li><a href="#org564a7a8">5. Adding fields to the form</a></li>
+<li><a href="#org633781a">6. <span class="todo TODO">TODO</span> Testing the license fields</a></li>
</ul>
</div>
</div>
-<div id="outline-container-org871ad58" class="outline-2">
-<h2 id="org871ad58"><span class="section-number-2">1</span> Modify Metadata</h2>
+<div id="outline-container-org758b923" class="outline-2">
+<h2 id="org758b923"><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
+<a href="http://covid19.genenetwork.org/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>.
+data are listed <a href="http://covid19.genenetwork.org/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). It is important to
+COVID-19 PubSeq website (or command line client). It is important to
understand that anyone, including you, can change that information!
</p>
</div>
</div>
-<div id="outline-container-org07e8755" class="outline-2">
-<h2 id="org07e8755"><span class="section-number-2">2</span> What is the schema?</h2>
+<div id="outline-container-orgec32c13" class="outline-2">
+<h2 id="orgec32c13"><span class="section-number-2">2</span> What is the schema?</h2>
<div class="outline-text-2" id="text-2">
<p>
The default metadata schema is listed <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml">here</a>.
@@ -274,8 +289,8 @@ The default metadata schema is listed <a href="https://github.com/arvados/bh20-s
</div>
</div>
-<div id="outline-container-org4857280" class="outline-2">
-<h2 id="org4857280"><span class="section-number-2">3</span> How is the website generated?</h2>
+<div id="outline-container-org2e487b2" class="outline-2">
+<h2 id="org2e487b2"><span class="section-number-2">3</span> How is the website generated?</h2>
<div class="outline-text-2" id="text-3">
<p>
Using the schema we use <a href="https://pypi.org/project/PyShEx/">pyshex</a> shex expressions and <a href="https://github.com/common-workflow-language/schema_salad">schema salad</a> to
@@ -285,13 +300,13 @@ All from that one metadata schema.
</div>
</div>
-<div id="outline-container-orge709ae2" class="outline-2">
-<h2 id="orge709ae2"><span class="section-number-2">4</span> Modifying the schema</h2>
+<div id="outline-container-orge4dfe84" class="outline-2">
+<h2 id="orge4dfe84"><span class="section-number-2">4</span> Modifying the schema</h2>
<div class="outline-text-2" id="text-4">
<p>
-One of the first things we wanted to do is to add a field for the data
-license. Initially we only support CC-4.0 as a license by default, but
-now we want to give uploaders the option to make it an even more
+One of the first things we want to do is to add a field for the data
+license. Initially we only supported CC-4.0 as a license, but
+we wanted to give uploaders the option to use an even more
liberal CC0 license. The first step is to find a good ontology term
for the field. Searching for `creative commons cc0 rdf' rendered this
useful <a href="https://creativecommons.org/ns">page</a>. We also find an <a href="https://wiki.creativecommons.org/wiki/CC_License_Rdf_Overview">overview</a> where CC0 is represented as URI
@@ -302,13 +317,148 @@ attributionName and attributionURL.
</p>
<p>
-<i>Note: work in progress</i>
+A minimal triple should be
+</p>
+
+<pre class="example">
+id xhtml:license &lt;http://creativecommons.org/licenses/by/4.0/&gt; .
+</pre>
+
+
+<p>
+Other suggestions are
+</p>
+
+<pre class="example">
+id dc:title "Description" .
+id cc:attributionName "Your Name" .
+id cc:attributionURL &lt;http://resource.org/id&gt;
+</pre>
+
+
+<p>
+and 'dc:source' which indicates the original source of any modified
+work, specified as a URI.
+The prefix 'cc:' is an abbreviation for <a href="http://creativecommons.org/ns">http://creativecommons.org/ns</a>#.
+</p>
+
+<p>
+Going back to the schema, where does it fit? Under host, sample,
+virus, technology or submitter block? It could fit under sample, but
+actually the license concerns the whole metadata block and sequence,
+so I think we can fit under its own license tag. For example
+</p>
+
+
+<p>
+id: placeholder
+</p>
+
+<pre class="example">
+license:
+ license_type: http://creativecommons.org/licenses/by/4.0/
+ attribution_title: "Sample ID"
+ attribution_name: "John doe, Joe Boe, Jonny Oe"
+ attribution_url: http://covid19.genenetwork.org/id
+ attribution_source: https://www.ncbi.nlm.nih.gov/pubmed/323088888
+</pre>
+
+
+<p>
+So, let's update the example. Notice the license info is optional - if it is missing
+we just assume the default CC-4.0.
+</p>
+
+<p>
+One thing that is interesting is that in the name space <a href="https://creativecommons.org/ns">https://creativecommons.org/ns</a> there
+is no mention of a title. I think it is useful, however, because we have no such field.
+So, we'll add it simply as a title field. Now the draft schema is
</p>
+
+<div class="org-src-container">
+<pre class="src src-js">- name: licenseSchema
+ type: record
+ fields:
+ license_type:
+ doc: License types as refined in https://wiki.creativecommons.org/images/d/d6/Ccrel-1.0.pdf
+ type: string?
+ jsonldPredicate:
+ _id: https://creativecommons.org/ns#License
+ title:
+ doc: Attribution title related to license
+ type: string?
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_001167
+ attribution_url:
+ doc: Attribution URL related to license
+ type: string?
+ jsonldPredicate:
+ _id: https://creativecommons.org/ns#Work
+ attribution_source:
+ doc: Attribution source URL
+ type: string?
+ jsonldPredicate:
+ _id: https://creativecommons.org/ns#Work
+</pre>
+</div>
+
+<p>
+Now, we are no ontology experts, right? So, next we submit a patch to
+our source tree and ask for feedback before wiring it up in the data
+entry form. The pull request was submitted <a href="https://github.com/arvados/bh20-seq-resource/pull/97">here</a> and reviewed on the
+gitter channel and I merged it.
+</p>
+</div>
</div>
+
+<div id="outline-container-org564a7a8" class="outline-2">
+<h2 id="org564a7a8"><span class="section-number-2">5</span> Adding fields to the form</h2>
+<div class="outline-text-2" id="text-5">
+<p>
+To add the new fields to the form we have to modify it a little. If we
+go to the upload form we need to add the license box. The schema is
+loaded in <a href="https://github.com/arvados/bh20-seq-resource/blob/a0c8ebd57b875f265e8b0efec4abfaf892eb6c45/bh20simplewebuploader/main.py#L229">main.py</a> in the 'generate<sub>form</sub>' function.
+</p>
+
+<p>
+With this <a href="https://github.com/arvados/bh20-seq-resource/commit/b9691c7deae30bd6422fb7b0681572b7b6f78ae3">patch</a> the website adds the license input fields on the form.
+</p>
+
+<p>
+Finally, to make RDF output work we need to add expressions to bh20seq-shex.rdf. This
+was done with this <a href="https://github.com/arvados/bh20-seq-resource/commit/f4ed46dae20abe5147871495ede2d6ac2b0854bc">patch</a>. In the end we decided to use the Dublin core title,
+<a href="http://purl.org/metadata/dublin_core_elements#Title">http://purl.org/metadata/dublin_core_elements#Title</a>:
+</p>
+
+<div class="org-src-container">
+<pre class="src src-js">:licenseShape{
+ cc:License xsd:string;
+ dc:Title xsd:string ?;
+ cc:attributionName xsd:string ?;
+ cc:attributionURL xsd:string ?;
+ cc:attributionSource xsd:string ?;
+}
+</pre>
+</div>
+
+<p>
+Note that cc:AttributionSource is not really defined in the cc standard.
+</p>
+
+<p>
+When pushing the license info we discovered the workflow broke because
+the existing data had no licensing info. So we changed the license
+field to be optional - a missing license assumes it is CC-BY-4.0.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org633781a" class="outline-2">
+<h2 id="org633781a"><span class="section-number-2">6</span> <span class="todo TODO">TODO</span> Testing the license fields</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 2020-07-12 Sun 06:24</small>.
+<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-16 Thu 03:27</small>.
</div>
</body>
</html>
generated by cgit v1.2.3 (git 2.44.0) at 2024-05-19 10:20:35 +0000