{
  "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/2010/02/22/further-statistics-on-papers-citing-cdk.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/10.59350/65fss-f1y18",
      "url": "https://chem-bla-ics.linkedchemistry.info/2010/02/22/further-statistics-on-papers-citing-cdk.html",
      "title": "Further statistics on the papers citing the CDK",
      "content_html": "<p>I already gave a <a href=\"https://chem-bla-ics.linkedchemistry.info/2010/02/21/wordle-of-titles-of-20-most-recent.html\">wordle <i class=\"fa-solid fa-recycle fa-xs\"></i></a> of the titles of papers citing the\n<a href=\"http://pubs.acs.org/doi/abs/10.1021/ci025584y\">first CDK paper</a>. Below follows some additional statistics: the number of papers that use a particular\n<a href=\"http://cdk.sf.net/\">CDK</a> package (51). Now, this numbers are a bit rough, and surely any paper that uses the CDK is bound to use the IO or\nSMILES package too. Additionally, for 10 papers I was not sure what CDK functionality they used, so I assigned those to the root package.</p>\n\n<div class=\"language-plaintext highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>org.openscience.cdk.qsar: 12 (~20%)\norg.openscience.cdk: 10\norg.openscience.cdk.fingerprint: 9\norg.openscience.cdk.isomorphism: 6\norg.openscience.cdk.similarity: 3\norg.openscience.cdk.smiles: 2\norg.openscience.cdk.io.cml: 2\norg.openscience.cdk.model.builder3d: 2\norg.openscience.cdk.ringsearch: 2\norg.openscience.cdk.tools: 2\norg.openscience.cdk.render: 1\norg.openscience.cdk.structgen: 1\norg.openscience.cdk.graph.matrix: 1\norg.openscience.cdk.io: 1\n</code></pre></div></div>\n\n<p>From this we learn what parts of the CDK are used. From the various CDK Literature blogs (<a href=\"http://chem-bla-ics.blogspot.com/2007/01/cdk-literature-1.html\">#1</a>,\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2007/07/14/cdk-literature-2.html\">#2 <i class=\"fa-solid fa-recycle fa-xs\"></i></a>, <a href=\"http://chem-bla-ics.blogspot.com/2008/01/cdk-literature-3.html\">#3</a>,\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2008/01/06/cdk-literature-4.html\">#4 <i class=\"fa-solid fa-recycle fa-xs\"></i></a>, and <a href=\"http://chem-bla-ics.blogspot.com/2008/07/cdk-literature-5.html\">#5</a>)\nI already knew the the descriptor calculation was much used, as well as the fingerprinter and the isomorphism checker which also provide the\nmaximum-common substructure functionality. What I was not aware of, is the our 3D model builder had been used in published studies too,\nwhich was a pleasant surprise.</p>\n\n<p>These numbers are based on 51 papers where CDK functionality was used, but you may be aware that <a href=\"http://isiwebofknowledge.com/products_tools/multidisciplinary/webofscience/\">Web-of-Science</a>\nhas 84 papers citing the first CDK paper. Of these, only 78 are actually in their database (which I don’t quite understand). Also, at least some\n10 papers cite the CDK, but do not use it, and a few papers cite the CDK where they actually use <a href=\"http://www.jmol.org/\">Jmol</a>. I also have to\nsay, that for a curated citation database, I too often have to send in bug reports, but I cannot estimate to what extend that affects these numbers.</p>\n\n<p>What does effect these numbers, is that some papers do not explicitly cite the CDK through one of the two papers, but only the website, or not\nat all (yes, that <a href=\"http://www.nature.com/nchembio/journal/v5/n8/full/nchembio.187.html\">happens</a>, but it nicely balances out with papers citing\nthe CDK but using Jmol :).</p>\n\n<p>Well, I’m curious what the statistics will say about the <a href=\"http://www.ingentaconnect.com/content/ben/cpd/2006/00000012/00000017/art00005\">second CDK paper</a>,\nand the <a href=\"http://www.mdpi.com/1420-3049/5/1/93/\">JChemPaint paper</a> which is based on the CDK too.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., &#38; Willighagen, E. (2003). The Chemistry Development Kit (CDK):  An Open-Source Java Library for Chemo- and Bioinformatics. <i>Journal of Chemical Information and Computer Sciences</i>, <i>43</i>(2), 493–500. https://doi.org/10.1021/ci025584y <a href=\"https://doi.org/10.1021/CI025584Y\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1021/CI025584Y\">Scholia</a></div>\n  </div>",
      "summary": "I already gave a wordle of the titles of papers citing the first CDK paper. Below follows some additional statistics: the number of papers that use a particular CDK package (51). Now, this numbers are a bit rough, and surely any paper that uses the CDK is bound to use the IO or SMILES package too. Additionally, for 10 papers I was not sure what CDK functionality they used, so I assigned those to the root package.",
      
      "date_published": "2010-02-22T00:00:00+00:00",
      "date_modified": "2026-09-27T00:00:00+00:00",
      "tags": ["cdk"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1021/CI025584Y", "doi": "10.1021/CI025584Y"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}