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authorPjotr Prins2020-07-15 11:43:35 +0100
committerGitHub2020-07-15 11:43:35 +0100
commita0c8ebd57b875f265e8b0efec4abfaf892eb6c45 (patch)
treeb5477179d66540ab25634295112a2df47df30e27 /doc
parent3dd94e87c25ff0b2942dc59c919a9e6e45fe45be (diff)
parentb5e38b960c380f0f7868d8fc4038ea3c3a0c52ee (diff)
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Merge pull request #97 from pjotrp/master
Add license metadata to record
Diffstat (limited to 'doc')
-rw-r--r--doc/blog/using-covid-19-pubseq-part5.org68
-rw-r--r--doc/web/about.html143
2 files changed, 135 insertions, 76 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part5.org b/doc/blog/using-covid-19-pubseq-part5.org
index fe1908a..4b0ea64 100644
--- a/doc/blog/using-covid-19-pubseq-part5.org
+++ b/doc/blog/using-covid-19-pubseq-part5.org
@@ -40,7 +40,7 @@ All from that one metadata schema.
* Modifying the schema
-One of the first things we wanted to do is to add a field for the data
+One of the first things we want 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
liberal CC0 license. The first step is to find a good ontology term
@@ -51,4 +51,70 @@ attribution license https://creativecommons.org/licenses/by/4.0/.
According to this [[https://wiki.creativecommons.org/images/d/d6/Ccrel-1.0.pdf][document]] we should really also add fields for
attributionName and attributionURL.
+A minimal triple should be
+
+: id xhtml:license <http://creativecommons.org/licenses/by/4.0/> .
+
+Other suggestions are
+
+: id dc:title "Description" .
+: id cc:attributionName "Your Name" .
+: id cc:attributionURL <http://resource.org/id>
+
+and 'dc:source' which indicates the original source of any modified
+work, specified as a URI.
+The prefix 'cc:' is an abbreviation for http://creativecommons.org/ns#.
+
+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
+
+
+id: placeholder
+
+: 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
+
+So, let's update the example. Notice the license info is optional - if it is missing
+we just assume the default CC-4.0.
+
+One thing that is interesting is that in the name space https://creativecommons.org/ns 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
+
+#+BEGIN_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
+#+END_SRC
+
+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 here FIXME.
+
/Note: work in progress/
diff --git a/doc/web/about.html b/doc/web/about.html
index c907e6c..9b16c92 100644
--- a/doc/web/about.html
+++ b/doc/web/about.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 08:27 -->
+<!-- 2020-07-12 Sun 06:29 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>About/FAQ</title>
@@ -161,19 +161,6 @@
.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;
@@ -198,7 +185,7 @@
@licstart The following is the entire license notice for the
JavaScript code in this tag.
-Copyright (C) 2012-2020 Free Software Foundation, Inc.
+Copyright (C) 2012-2018 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
@@ -247,29 +234,29 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
-<li><a href="#org783b5e9">1. What is the 'public sequence resource' about?</a></li>
-<li><a href="#org2c0bcfd">2. Who created the public sequence resource?</a></li>
-<li><a href="#org34070d3">3. How does the public sequence resource compare to other data resources?</a></li>
-<li><a href="#org64a9493">4. Why should I upload my data here?</a></li>
-<li><a href="#orgf898e7f">5. Why should I not upload by data here?</a></li>
-<li><a href="#org828e164">6. How does the public sequence resource work?</a></li>
-<li><a href="#org7b0d03f">7. Who uses the public sequence resource?</a></li>
-<li><a href="#org31aaf23">8. Is this about open data?</a></li>
-<li><a href="#orgb376b6c">9. Is this about free software?</a></li>
-<li><a href="#orgf19cd96">10. How do I upload raw data?</a></li>
-<li><a href="#orgebfed00">11. How do I change metadata?</a></li>
-<li><a href="#orge2aecf8">12. How do I change the work flows?</a></li>
-<li><a href="#orgd45b3bc">13. How do I change the source code?</a></li>
-<li><a href="#org2bb9455">14. Should I choose CC-BY or CC0?</a></li>
-<li><a href="#org62bf23f">15. How do I deal with private data and privacy?</a></li>
-<li><a href="#org40c6da0">16. How do I communicate with you?</a></li>
-<li><a href="#org1f27c44">17. Who are the sponsors?</a></li>
+<li><a href="#orgac6ad8b">1. What is the 'public sequence resource' about?</a></li>
+<li><a href="#org0c21c2e">2. Who created the public sequence resource?</a></li>
+<li><a href="#org3fb8cb3">3. How does the public sequence resource compare to other data resources?</a></li>
+<li><a href="#org6cd9ea2">4. Why should I upload my data here?</a></li>
+<li><a href="#org0b6e3fb">5. Why should I not upload by data here?</a></li>
+<li><a href="#org3eb3a4e">6. How does the public sequence resource work?</a></li>
+<li><a href="#org7a397f5">7. Who uses the public sequence resource?</a></li>
+<li><a href="#org92cb008">8. Is this about open data?</a></li>
+<li><a href="#org232d6fa">9. Is this about free software?</a></li>
+<li><a href="#orgd93869f">10. How do I upload raw data?</a></li>
+<li><a href="#org88e8b0a">11. How do I change metadata?</a></li>
+<li><a href="#orgd04b8f8">12. How do I change the work flows?</a></li>
+<li><a href="#org5d1ee05">13. How do I change the source code?</a></li>
+<li><a href="#orgae6461b">14. Should I choose CC-BY or CC0?</a></li>
+<li><a href="#org3ea90a9">15. How do I deal with private data and privacy?</a></li>
+<li><a href="#org7ff7106">16. How do I communicate with you?</a></li>
+<li><a href="#org9566fa7">17. Who are the sponsors?</a></li>
</ul>
</div>
</div>
-<div id="outline-container-org783b5e9" class="outline-2">
-<h2 id="org783b5e9"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2>
+<div id="outline-container-orgac6ad8b" class="outline-2">
+<h2 id="orgac6ad8b"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2>
<div class="outline-text-2" id="text-1">
<p>
The <b>public sequence resource</b> aims to provide a generic and useful
@@ -280,17 +267,18 @@ sequence comparison and protein prediction.
</div>
</div>
-<div id="outline-container-org2c0bcfd" class="outline-2">
-<h2 id="org2c0bcfd"><span class="section-number-2">2</span> Who created the public sequence resource?</h2>
+<div id="outline-container-org0c21c2e" class="outline-2">
+<h2 id="org0c21c2e"><span class="section-number-2">2</span> Who created the public sequence resource?</h2>
<div class="outline-text-2" id="text-2">
<p>
The <b>public sequence resource</b> is an initiative by <a href="https://github.com/arvados/bh20-seq-resource/graphs/contributors">bioinformatics</a> and
ontology experts who want to create something agile and useful for the
wider research community. The initiative started at the COVID-19
biohackathon in April 2020 and is ongoing. The main project drivers
-are Pjotr Prins (UTHSC), Peter Amstutz (Curii), Michael Crusoe (Common
-Workflow Language), Thomas Liener (consultant, formerly EBI) and
-Jerven Bolleman (Swiss Institute of Bioinformatics).
+are Pjotr Prins (UTHSC), Peter Amstutz (Curii), Andrea Guarracino
+(University of Rome Tor Vergata), Michael Crusoe (Common Workflow
+Language), Thomas Liener (consultant, formerly EBI), Erik Garrison
+(UCSC) and Jerven Bolleman (Swiss Institute of Bioinformatics).
</p>
<p>
@@ -301,8 +289,8 @@ wrangling experts. Thank you everyone!
</div>
</div>
-<div id="outline-container-org34070d3" class="outline-2">
-<h2 id="org34070d3"><span class="section-number-2">3</span> How does the public sequence resource compare to other data resources?</h2>
+<div id="outline-container-org3fb8cb3" class="outline-2">
+<h2 id="org3fb8cb3"><span class="section-number-2">3</span> How does the public sequence resource compare to other data resources?</h2>
<div class="outline-text-2" id="text-3">
<p>
The short version is that we use state-of-the-art practices in
@@ -312,17 +300,18 @@ to building out this resource!
</p>
<p>
-Importantly: all data is published under the <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons 4.0
-attribution license</a> which means it data can be published and workflows
-can run in public environments allowing for improved access for
-research and reproducible results. This contrasts with some other
-public resources, including GISAID.
+Importantly: all data is published under either the <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons
+4.0 attribution license</a> or the <a href="https://creativecommons.org/share-your-work/public-domain/cc0/">CC0 “No Rights Reserved” license</a> which
+means it data can be published and workflows can run in public
+environments allowing for improved access for research and
+reproducible results. This contrasts with some other public resources,
+including GISAID.
</p>
</div>
</div>
-<div id="outline-container-org64a9493" class="outline-2">
-<h2 id="org64a9493"><span class="section-number-2">4</span> Why should I upload my data here?</h2>
+<div id="outline-container-org6cd9ea2" class="outline-2">
+<h2 id="org6cd9ea2"><span class="section-number-2">4</span> Why should I upload my data here?</h2>
<div class="outline-text-2" id="text-4">
<ol class="org-ol">
<li>We champion truly shareable data without licensing restrictions - with proper
@@ -353,8 +342,8 @@ multiple resources.
</div>
</div>
-<div id="outline-container-orgf898e7f" class="outline-2">
-<h2 id="orgf898e7f"><span class="section-number-2">5</span> Why should I not upload by data here?</h2>
+<div id="outline-container-org0b6e3fb" class="outline-2">
+<h2 id="org0b6e3fb"><span class="section-number-2">5</span> Why should I not upload by data here?</h2>
<div class="outline-text-2" id="text-5">
<p>
Funny question. There are only good reasons to upload your data here
@@ -376,8 +365,8 @@ for bulk uploads!
</div>
</div>
-<div id="outline-container-org828e164" class="outline-2">
-<h2 id="org828e164"><span class="section-number-2">6</span> How does the public sequence resource work?</h2>
+<div id="outline-container-org3eb3a4e" class="outline-2">
+<h2 id="org3eb3a4e"><span class="section-number-2">6</span> How does the public sequence resource work?</h2>
<div class="outline-text-2" id="text-6">
<p>
On uploading a sequence with metadata it will automatically be
@@ -388,8 +377,8 @@ using workflows from the High Performance Open Biology Lab defined
</div>
</div>
-<div id="outline-container-org7b0d03f" class="outline-2">
-<h2 id="org7b0d03f"><span class="section-number-2">7</span> Who uses the public sequence resource?</h2>
+<div id="outline-container-org7a397f5" class="outline-2">
+<h2 id="org7a397f5"><span class="section-number-2">7</span> Who uses the public sequence resource?</h2>
<div class="outline-text-2" id="text-7">
<p>
The Swiss Institute of Bioinformatics has included this data in
@@ -397,14 +386,18 @@ The Swiss Institute of Bioinformatics has included this data in
</p>
<p>
+The Pantograph <a href="https://graph-genome.github.io/">viewer</a> uses PubSeq data for their visualisations.
+</p>
+
+<p>
<a href="https://uthsc.edu">UTHSC</a> and <a href="https://www.ornl.gov/news/ornl-fight-against-covid-19">ORNL</a> use COVID-19 PubSeq data for protein prediction and
drug development.
</p>
</div>
</div>
-<div id="outline-container-org31aaf23" class="outline-2">
-<h2 id="org31aaf23"><span class="section-number-2">8</span> Is this about open data?</h2>
+<div id="outline-container-org92cb008" class="outline-2">
+<h2 id="org92cb008"><span class="section-number-2">8</span> Is this about open data?</h2>
<div class="outline-text-2" id="text-8">
<p>
All data is published under a <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons 4.0 attribution license</a>
@@ -414,8 +407,8 @@ data and store it for further processing.
</div>
</div>
-<div id="outline-container-orgb376b6c" class="outline-2">
-<h2 id="orgb376b6c"><span class="section-number-2">9</span> Is this about free software?</h2>
+<div id="outline-container-org232d6fa" class="outline-2">
+<h2 id="org232d6fa"><span class="section-number-2">9</span> Is this about free software?</h2>
<div class="outline-text-2" id="text-9">
<p>
Absolutely. Free software allows for fully reproducible pipelines. You
@@ -424,8 +417,8 @@ can take our workflows and data and run it elsewhere!
</div>
</div>
-<div id="outline-container-orgf19cd96" class="outline-2">
-<h2 id="orgf19cd96"><span class="section-number-2">10</span> How do I upload raw data?</h2>
+<div id="outline-container-orgd93869f" class="outline-2">
+<h2 id="orgd93869f"><span class="section-number-2">10</span> How do I upload raw data?</h2>
<div class="outline-text-2" id="text-10">
<p>
We are preparing raw sequence data pipelines (fastq and BAM). The
@@ -440,8 +433,8 @@ assembly variations into consideration. This is all work in progress.
</div>
</div>
-<div id="outline-container-orgebfed00" class="outline-2">
-<h2 id="orgebfed00"><span class="section-number-2">11</span> How do I change metadata?</h2>
+<div id="outline-container-org88e8b0a" class="outline-2">
+<h2 id="org88e8b0a"><span class="section-number-2">11</span> How do I change metadata?</h2>
<div class="outline-text-2" id="text-11">
<p>
See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>!
@@ -449,8 +442,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork
</div>
</div>
-<div id="outline-container-orge2aecf8" class="outline-2">
-<h2 id="orge2aecf8"><span class="section-number-2">12</span> How do I change the work flows?</h2>
+<div id="outline-container-orgd04b8f8" class="outline-2">
+<h2 id="orgd04b8f8"><span class="section-number-2">12</span> How do I change the work flows?</h2>
<div class="outline-text-2" id="text-12">
<p>
See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>!
@@ -458,8 +451,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork
</div>
</div>
-<div id="outline-container-orgd45b3bc" class="outline-2">
-<h2 id="orgd45b3bc"><span class="section-number-2">13</span> How do I change the source code?</h2>
+<div id="outline-container-org5d1ee05" class="outline-2">
+<h2 id="org5d1ee05"><span class="section-number-2">13</span> How do I change the source code?</h2>
<div class="outline-text-2" id="text-13">
<p>
Go to our <a href="https://github.com/arvados/bh20-seq-resource">source code repositories</a>, fork/clone the repository, change
@@ -469,8 +462,8 @@ many PRs we already merged.
</div>
</div>
-<div id="outline-container-org2bb9455" class="outline-2">
-<h2 id="org2bb9455"><span class="section-number-2">14</span> Should I choose CC-BY or CC0?</h2>
+<div id="outline-container-orgae6461b" class="outline-2">
+<h2 id="orgae6461b"><span class="section-number-2">14</span> Should I choose CC-BY or CC0?</h2>
<div class="outline-text-2" id="text-14">
<p>
Restrictive data licenses are hampering data sharing and reproducible
@@ -486,8 +479,8 @@ In all honesty: we prefer both data and software to be free.
</div>
</div>
-<div id="outline-container-org62bf23f" class="outline-2">
-<h2 id="org62bf23f"><span class="section-number-2">15</span> How do I deal with private data and privacy?</h2>
+<div id="outline-container-org3ea90a9" class="outline-2">
+<h2 id="org3ea90a9"><span class="section-number-2">15</span> How do I deal with private data and privacy?</h2>
<div class="outline-text-2" id="text-15">
<p>
A public sequence resource is about public data. Metadata can refer to
@@ -498,8 +491,8 @@ plan to combine identifiers with clinical data stored securely at
</div>
</div>
-<div id="outline-container-org40c6da0" class="outline-2">
-<h2 id="org40c6da0"><span class="section-number-2">16</span> How do I communicate with you?</h2>
+<div id="outline-container-org7ff7106" class="outline-2">
+<h2 id="org7ff7106"><span class="section-number-2">16</span> How do I communicate with you?</h2>
<div class="outline-text-2" id="text-16">
<p>
We use a <a href="https://gitter.im/arvados/pubseq?utm_source=share-link&amp;utm_medium=link&amp;utm_campaign=share-link">gitter channel</a> you can join.
@@ -507,8 +500,8 @@ We use a <a href="https://gitter.im/arvados/pubseq?utm_source=share-link&amp;utm
</div>
</div>
-<div id="outline-container-org1f27c44" class="outline-2">
-<h2 id="org1f27c44"><span class="section-number-2">17</span> Who are the sponsors?</h2>
+<div id="outline-container-org9566fa7" class="outline-2">
+<h2 id="org9566fa7"><span class="section-number-2">17</span> Who are the sponsors?</h2>
<div class="outline-text-2" id="text-17">
<p>
The main sponsors are listed in the footer. In addition to the time
@@ -519,7 +512,7 @@ for donating COVID-19 related compute time.
</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 08:26</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 2020-07-12 Sun 04:54</small>.
</div>
</body>
</html>
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