<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.3.4">Jekyll</generator><link href="https://chem-bla-ics.linkedchemistry.info/feed/by_tag/opencitations.xml" rel="self" type="application/atom+xml" /><link href="https://chem-bla-ics.linkedchemistry.info/" rel="alternate" type="text/html" /><updated>2026-07-18T13:36:15+00:00</updated><id>https://chem-bla-ics.linkedchemistry.info/feed/by_tag/opencitations.xml</id><title type="html">chem-bla-ics</title><subtitle>Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.</subtitle><author><name>Egon Willighagen</name></author><entry><title type="html">Adding citations between existing articles in Wikidata</title><link href="https://chem-bla-ics.linkedchemistry.info/2024/09/07/wikidata-citations.html" rel="alternate" type="text/html" title="Adding citations between existing articles in Wikidata" /><published>2024-09-07T00:00:00+00:00</published><updated>2024-09-07T00:00:00+00:00</updated><id>https://chem-bla-ics.linkedchemistry.info/2024/09/07/wikidata-citations</id><content type="html" xml:base="https://chem-bla-ics.linkedchemistry.info/2024/09/07/wikidata-citations.html"><![CDATA[<p>Scholarly articles provide context to the factualness of statements in <a href="https://wikidata.org/">Wikidata</a>,
similar to the <a href="https://en.wikipedia.org/wiki/Citation_needed">[citation needed]</a> in <a href="https://en.wikipedia.org/wiki/">Wikipedia</a>.
And just like the cited references in each scholarly article itself. The citation network is general seen
as an essential part of (doing) science, even without <a href="https://chem-bla-ics.linkedchemistry.info/tag/cito">citation intention annotation</a>.
Nowadays, citations are mostly open, but this took very serious lobbying by the <a href="https://i4oc.org/">Initiative for Open Citations</a> and
<a href="https://chem-bla-ics.linkedchemistry.info/2018/11/17/join-me-in-encouraging-acs-to-join.html">not every publisher reacted immediately</a>.
But now that they are open, projects like <a href="https://opencitations.net/">OpenCitations</a> are making this citation
network FAIR.</p>

<p>Therefore, when an article is cited as reference in Wikidata, I think that the articles (and other research output)
cited in that article is part of the reference. After all, it is really hard to understand any article without the details
in the cited articles. So, getting these citations between article into Wikidata deepens the knowledge captured
by Wikidata. Of course, Wikidata is also one of the few places where we can capture the citation intentions at all.</p>

<p>Adding these citations manually is cumbersome but <a href="https://chem-bla-ics.linkedchemistry.info/2023/08/08/history-provenance-detail.html">sometimes needed</a>
as these citations are not open or not FAIR yet. Fortunately, in many cases we can automate the process, for
which I wrote a <a href="https://chem-bla-ics.linkedchemistry.info/tag/bioclipse">Bacting</a>-cased
<a href="https://github.com/egonw/ons-wikidata/blob/main/OpenCitations/quickstatements.groovy">script</a>.
Until recently, the script takes as input a single DOI or a list of DOIs as input, and for each DOI
looks up in OpenCitations if it cites other article DOIs and is cited by other DOIs. For the
cited and citing DOIs it checks if those are in Wikidata and (only) if they are in Wikidata,
then it create QuickStatements. The result can look like <a href="https://www.wikidata.org/wiki/Q91911528#P2860">this</a>:</p>

<p><img src="/assets/images/opencitationsImport.png" alt="" /></p>

<p>The script also needs a OpenCitation token, which you can <a href="https://opencitations.net/querying">get here</a>.
This is how I run the code from the command line (with the token in the <code class="language-plaintext highlighter-rouge">TOKEN</code> environment variable),
for a single DOI:</p>

<div class="language-shell highlighter-rouge"><div class="highlight"><pre class="highlight"><code>groovy quickstatements.groovy <span class="nt">-t</span> <span class="k">${</span><span class="nv">TOKEN</span><span class="k">}</span> <span class="nt">-d</span> 10.1002/JLAC.18721620110 | <span class="nb">tee </span>output.qs
</code></pre></div></div>

<p>A list of DOIs is provided as a text file, with one DOI on one line. I then use the <code class="language-plaintext highlighter-rouge">-l</code> parameter
(oh, here DOIs of works by <a href="https://en.wikipedia.org/wiki/Shyamala_Gopalan">Shyamala Gopalan</a>, mother of
<a href="https://en.wikipedia.org/wiki/Kamala_Harris">Kamala Harris</a>):</p>

<div class="language-shell highlighter-rouge"><div class="highlight"><pre class="highlight"><code>groovy quickstatements.groovy <span class="nt">-t</span> <span class="k">${</span><span class="nv">TOKEN</span><span class="k">}</span> <span class="nt">-l</span> harris_dois.txt | <span class="nb">tee </span>output.qs
</code></pre></div></div>

<p>But last weekend I created a new feature. To enrich the profiles of authors, for example Nobel Prize
winners, mothers of, or <a href="https://scholia.toolforge.org/author/Q76784">famous</a> <a href="https://scholia.toolforge.org/author/Q80956">chemists</a>,
previously I would create a list of DOIs, now I have the script do that:</p>

<p>So, today I could add the citation network for any arbitraty author, e.g. <a href="https://en.wikipedia.org/wiki/Carolyn_Bertozzi">Carolyn Bertozzi</a>,
I just pass the Wikidata QID:</p>

<div class="language-shell highlighter-rouge"><div class="highlight"><pre class="highlight"><code>groovy quickstatements.groovy <span class="nt">-t</span> <span class="k">${</span><span class="nv">TOKEN</span><span class="k">}</span> <span class="nt">-a</span> Q7442 | <span class="nb">tee </span>output.qs
</code></pre></div></div>

<p>I can imagine that in the future the script will have more such options, to do the same
for many authors at some affiliation, or all DOIs for a certain journal.</p>]]></content><author><name>Egon Willighagen</name></author><category term="wikidata" /><category term="bioclipse" /><category term="opencitations" /><category term="justdoi:10.1002/JLAC.18721620110" /><summary type="html"><![CDATA[Scholarly articles provide context to the factualness of statements in Wikidata, similar to the [citation needed] in Wikipedia. And just like the cited references in each scholarly article itself. The citation network is general seen as an essential part of (doing) science, even without citation intention annotation. Nowadays, citations are mostly open, but this took very serious lobbying by the Initiative for Open Citations and not every publisher reacted immediately. But now that they are open, projects like OpenCitations are making this citation network FAIR.]]></summary><media:thumbnail xmlns:media="http://search.yahoo.com/mrss/" url="https://chem-bla-ics.linkedchemistry.info/assets/images/opencitationsImport.png" /><media:content medium="image" url="https://chem-bla-ics.linkedchemistry.info/assets/images/opencitationsImport.png" xmlns:media="http://search.yahoo.com/mrss/" /></entry><entry><title type="html">Winter solstice challenge: what is your Open Knowledge score?</title><link href="https://chem-bla-ics.linkedchemistry.info/2017/11/26/winter-solstice-challenge-what-is-your.html" rel="alternate" type="text/html" title="Winter solstice challenge: what is your Open Knowledge score?" /><published>2017-11-26T00:00:00+00:00</published><updated>2017-11-26T00:00:00+00:00</updated><id>https://chem-bla-ics.linkedchemistry.info/2017/11/26/winter-solstice-challenge-what-is-your</id><content type="html" xml:base="https://chem-bla-ics.linkedchemistry.info/2017/11/26/winter-solstice-challenge-what-is-your.html"><![CDATA[<p><img src="/assets/images/Robert_Snache_-_Spirithands.net_-_Winter_Solstice_Lunar_Eclipse_Startrails_(by).jpg" style="width: 30%; display: block; margin-left: auto; margin-right: auto; float: right" alt="Photo of a time laps of a starry night, making the stars show as lines in the sky. Source: Wikimedia, CC-BY 2.0, https://commons.wikimedia.org/wiki/File:Robert_Snache_-_Spirithands.net_-_Winter_Solstice_Lunar_Eclipse_Startrails_(by).jpg)" />
Hi all, welcome to this winter solstice challenge! Umm, to not give our southern hemisphere colleagues
not a disadvantage, as their winter solstice has already passes, you’re up for a summer solstice challenge!</p>

<h2 id="introduction">Introduction</h2>

<p>So, you know <a href="http://impactstory.org/">ImpactStory</a> and <a href="http://altmetric.com/">Altmetric.com</a> (if not,
<a href="https://chem-bla-ics.blogspot.com/search?q=impactstory&amp;max-results=20&amp;by-date=true">browse</a>
<a href="https://chem-bla-ics.blogspot.com/search?q=altmetric&amp;max-results=20&amp;by-date=true">my blog</a>);
these are wonderful tools to see what people are doing with your work. I hope you already know about
<a href="http://opencitations.net/">OpenCitations</a>, a collaboration of publishers, CrossRef, and many others, to
make all citation data available. They just passed the 50% milestone, congratulations on that amazing
achievement! For the younger scientists it may be worth realizing that for the past 20 years, at least,
this data was copyrighted and not to be used unless you paid. Elsevier is, BTW,
<a href="https://opencitations.wordpress.com/2017/11/24/elsevier-references-dominate-those-that-are-not-open-at-crossref/">the major culprit</a>
still claiming IP on this, but RT this if you are surprised.</p>

<p>So, the reason I introduce both ImpactStory and OpenCitations is the following. Scientific articles are
data and knowledge dense documents. If we did not redirect the reader to other literature. That may give
a more complete sketch of the context, describe a measurement protocol, describe how certain knowledge
was derived, etc. Therefore, just having your article Open Access is not enough: the articles you cite
should be Open Access too. That’s the next phase if really making an effort to have
<a href="https://en.wikisource.org/wiki/Universal_Declaration_of_Human_Rights">all of humanity benefit from the fruits of science</a>.</p>

<p>I know it is hard already to calculate a “Open Access” score, though ImpactStory does a great job at
that! So, calculating this for your paper and the papers those papers cite is even harder. You may
need to brush up your algorithm and programming skills.</p>

<h2 id="eligibility">Eligibility</h2>

<p>Anyone is allowed to participate. Submission of your entry is done online, e.g. in your blog, in a public
write up, or even a <a href="https://en.wikipedia.org/wiki/Open_notebook_science">open notebook</a>!
However, you need at least on citable research object. That is, it
needs a DOI. Otherwise, I cannot give you the prize (see below). The score should be based on all your
products. Bonus points for those who include software and data citations. Excluding citable object to
boost your score (for example, I would have to exclude my book chapters), is seen as cheating the system.</p>

<p><img src="/assets/images/800px-Global_key-route_main_paths_for_a_citation_network.svg.png" style="width: 40%; display: block; margin-left: auto; margin-right: auto; float: right" alt="Your article B may cite three articles (C, D, J) but article D also cited articles (F, I). So, your Open Knowledge score is recursive. Source: Wikipedia, CC-BY-SA 4.0, https://commons.wikimedia.org/wiki/File:Global_key-route_main_paths_for_a_citation_network.svg" /></p>

<h2 id="depth">Depth</h2>

<p>Calculating your Open Knowledge score can be done at multiple levels. After all, your article depends
(cites) articles, and your software depends on libraries, but those cited articles and software
dependencies recursively also cite articles and/or software. The complexity is non-trivial, making it
a perfect solstice challenge indeed!</p>

<h2 id="prizes">Prizes</h2>

<p>The prize I have to offer is my continued commitment to Open Science, but that you already get for
free and may not be enough boon. So, instead, soon after the winter/summer solstice at the end of this year,
I will blog about your research boosting your <a href="https://en.wikipedia.org/wiki/Altmetrics">#altmetrics</a>
scores. Yes, I will actually read and try to understand it!</p>

<p>And because there is the results and the method, neither of which exist yet, there are two categories! I just
<strong><em>doubled your chance</em></strong> of winning! That’s because humanity is worth it! One prize for the best tool to calculated
your Open Knowledge score, and one prize for the researcher with the highest score.</p>

<h2 id="audience-prize">Audience Prize</h2>

<p>If someone feels a need to organize an audience prize, this is very much encouraged! (Assuming Open approaches, of course :)</p>]]></content><author><name>Egon Willighagen</name></author><category term="solstice" /><category term="altmetrics" /><category term="opencitations" /><summary type="html"><![CDATA[Hi all, welcome to this winter solstice challenge! Umm, to not give our southern hemisphere colleagues not a disadvantage, as their winter solstice has already passes, you’re up for a summer solstice challenge!]]></summary><media:thumbnail xmlns:media="http://search.yahoo.com/mrss/" url="https://chem-bla-ics.linkedchemistry.info/assets/images/Robert_Snache_-_Spirithands.net_-_Winter_Solstice_Lunar_Eclipse_Startrails_(by).jpg" /><media:content medium="image" url="https://chem-bla-ics.linkedchemistry.info/assets/images/Robert_Snache_-_Spirithands.net_-_Winter_Solstice_Lunar_Eclipse_Startrails_(by).jpg" xmlns:media="http://search.yahoo.com/mrss/" /></entry></feed>