{
  "version": "https://jsonfeed.org/version/1.1",
  "title": "chem-bla-ics",
  "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.",
  "home_page_url": "https://chem-bla-ics.linkedchemistry.info/",
  "feed_url": "https://chem-bla-ics.linkedchemistry.info/2024/09/07/wikidata-citations.json",
  "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png",
  "language": "en",
  "authors": [
    {
      "name": "Egon Willighagen",
      "url": "https://orcid.org/0000-0001-7542-0286",
      "_orcid": "0000-0001-7542-0286"
    }
  ],
  "items": [

    {
      "id": "https://doi.org/10.59350/7hjzg-ngr66",
      "url": "https://chem-bla-ics.linkedchemistry.info/2024/09/07/wikidata-citations.html",
      "title": "Adding citations between existing articles in Wikidata",
      "content_html": "<p>Scholarly articles provide context to the factualness of statements in <a href=\"https://wikidata.org/\">Wikidata</a>,\nsimilar to the <a href=\"https://en.wikipedia.org/wiki/Citation_needed\">[citation needed]</a> in <a href=\"https://en.wikipedia.org/wiki/\">Wikipedia</a>.\nAnd just like the cited references in each scholarly article itself. The citation network is general seen\nas an essential part of (doing) science, even without <a href=\"https://chem-bla-ics.linkedchemistry.info/tag/cito\">citation intention annotation</a>.\nNowadays, citations are mostly open, but this took very serious lobbying by the <a href=\"https://i4oc.org/\">Initiative for Open Citations</a> and\n<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>.\nBut now that they are open, projects like <a href=\"https://opencitations.net/\">OpenCitations</a> are making this citation\nnetwork FAIR.</p>\n\n<p>Therefore, when an article is cited as reference in Wikidata, I think that the articles (and other research output)\ncited in that article is part of the reference. After all, it is really hard to understand any article without the details\nin the cited articles. So, getting these citations between article into Wikidata deepens the knowledge captured\nby Wikidata. Of course, Wikidata is also one of the few places where we can capture the citation intentions at all.</p>\n\n<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>\nas these citations are not open or not FAIR yet. Fortunately, in many cases we can automate the process, for\nwhich I wrote a <a href=\"https://chem-bla-ics.linkedchemistry.info/tag/bioclipse\">Bacting</a>-cased\n<a href=\"https://github.com/egonw/ons-wikidata/blob/main/OpenCitations/quickstatements.groovy\">script</a>.\nUntil recently, the script takes as input a single DOI or a list of DOIs as input, and for each DOI\nlooks up in OpenCitations if it cites other article DOIs and is cited by other DOIs. For the\ncited and citing DOIs it checks if those are in Wikidata and (only) if they are in Wikidata,\nthen it create QuickStatements. The result can look like <a href=\"https://www.wikidata.org/wiki/Q91911528#P2860\">this</a>:</p>\n\n<p><img src=\"/assets/images/opencitationsImport.png\" alt=\"\" /></p>\n\n<p>The script also needs a OpenCitation token, which you can <a href=\"https://opencitations.net/querying\">get here</a>.\nThis 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),\nfor a single DOI:</p>\n\n<div class=\"language-shell highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>groovy quickstatements.groovy <span class=\"nt\">-t</span> <span class=\"k\">${</span><span class=\"nv\">TOKEN</span><span class=\"k\">}</span> <span class=\"nt\">-d</span> 10.1002/JLAC.18721620110 | <span class=\"nb\">tee </span>output.qs\n</code></pre></div></div>\n\n<p>A list of DOIs is provided as a text file, with one DOI on one line. I then use the <code class=\"language-plaintext highlighter-rouge\">-l</code> parameter\n(oh, here DOIs of works by <a href=\"https://en.wikipedia.org/wiki/Shyamala_Gopalan\">Shyamala Gopalan</a>, mother of\n<a href=\"https://en.wikipedia.org/wiki/Kamala_Harris\">Kamala Harris</a>):</p>\n\n<div class=\"language-shell highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>groovy quickstatements.groovy <span class=\"nt\">-t</span> <span class=\"k\">${</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\n</code></pre></div></div>\n\n<p>But last weekend I created a new feature. To enrich the profiles of authors, for example Nobel Prize\nwinners, mothers of, or <a href=\"https://scholia.toolforge.org/author/Q76784\">famous</a> <a href=\"https://scholia.toolforge.org/author/Q80956\">chemists</a>,\npreviously I would create a list of DOIs, now I have the script do that:</p>\n\n<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>,\nI just pass the Wikidata QID:</p>\n\n<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\n</code></pre></div></div>\n\n<p>I can imagine that in the future the script will have more such options, to do the same\nfor many authors at some affiliation, or all DOIs for a certain journal.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Kekulé, Aug. (1872). Ueber einige Condensationsproducte des Aldehyds. <i>Justus Liebigs Annalen Der Chemie</i>, <i>162</i>(1), 77–124. https://doi.org/10.1002/jlac.18721620110 <a href=\"https://doi.org/10.1002/JLAC.18721620110\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1002/JLAC.18721620110\">Scholia</a></div>\n  </div>",
      "summary": "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.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/opencitationsImport.png",
      "date_published": "2024-09-07T00:00:00+00:00",
      "date_modified": "2024-09-07T00:00:00+00:00",
      "tags": ["wikidata","bioclipse","opencitations"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1002/JLAC.18721620110", "doi": "10.1002/JLAC.18721620110"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}
