{
  "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/2010/12/30/text-mining-chemistry-from-dutch-or.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/k1tea-hnb50",
      "url": "https://chem-bla-ics.linkedchemistry.info/2010/12/30/text-mining-chemistry-from-dutch-or.html",
      "title": "Text mining chemistry from Dutch or Swedish texts",
      "content_html": "<p><a href=\"http://oscar3-chem.sf.net/\">Oscar</a> is a text miner. It mines in text for chemistry.\n<a href=\"https://bitbucket.org/wwmm/oscar4/\">Oscar4</a> is the next iteration of Oscar\ncode that I worked on in the past three months, with Lezan, Sam, and David. I blogged about\naspects of Oscar4 at several occasions:</p>\n\n<ul>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2010/10/15/working-on-oscar-for-three-months.html\">Working on Oscar for three months <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2010/10/21/oscar-text-mining-in-taverna.html\">Oscar text mining in Taverna <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2010/10/26/multiple-unit-test-inheritance-with.html\">Multiple unit test inheritance with JExample <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2010/10/28/oscar4-java-api-chemical-name.html\">Oscar4 Java API: chemical name dictionaries <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2010/11/18/oscar4-command-line-utilities.html\">Oscar4 command line utilities <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n  <li><a href=\"http://chem-bla-ics.blogspot.com/2010/11/installing-oscar.html\">Installing Oscar</a></li>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2010/11/29/adding-new-dictionary-to-oscar.html\">Adding a new dictionary to Oscar <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2010/12/11/status-update-on-bjoc-analysis-with.html\">Status update on BJOC analysis with Oscar and ChemicalTagger <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2010/12/11/status-update-on-bjoc-analysis-with_11.html\">Status update on BJOC analysis with Oscar and ChemicalTagger #2 <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2010/12/11/supramolecular-chemistry.html\">Supramolecular chemistry <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2010/12/23/status-update-on-bjoc-analysis-with_23.html\">Status update on BJOC analysis with Oscar and ChemicalTagger #3 <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2010/12/26/oscar-training-data-models-etc.html\">Oscar: training data, models, etc <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n</ul>\n\n<p>These posts will server is a some initial critical mass for a draft report I plan to finish\ntoday. I might have to blog some further posts with diagrams, here and there. This post is\nactually one of them, and discusses something where Oscar can be expected to go next, now\nthat the design is cleaned up (though this effort is not halted now) and it has become\npossible again to extend it. The over <a href=\"https://hudson.ch.cam.ac.uk/job/oscar4/lastBuild/testReport/\">250 unit tests</a>\nmake this a lot easier too.</p>\n\n<p>One aspect where I expect Oscar to go in 2011 is the support for other languages. To a very\nlarge extend this is based on multi-language support in the dictionaries, as well as having\ntraining data in a particular language. This also provides some context to my earlier post\nabout the <a href=\"https://chem-bla-ics.linkedchemistry.info/2010/12/26/oscar-training-data-models-etc.html\">need for a Oscar training data repository <i class=\"fa-solid fa-recycle fa-xs\"></i></a>.</p>\n\n<p>This extension opens a number of options: analysis of patent literature in other languages,\nmonitoring of press releases in other languages, and news items in local news papers, etc.\nFor example, it could analyse <a href=\"http://www.c2w.nl/energierijke-gistcel.119621.lynkx\">this C2W news item</a>\non <a href=\"http://en.wikipedia.org/wiki/Yeast\">yeast</a> cells:</p>\n\n<p><img src=\"/assets/images/c2w.png\" alt=\"\" /></p>\n\n<p>There are many use cases for such localized text mining. And it surely matters for determining\nthe impact of research.</p>\n\n<p>Oscar has various places where language specifics are found. For example, in tokenization of a\ntext. One step here is the detection of sentence ends. This is done in most western languages\nwith a period, exclamation mark, question mark, etc. But periods (dots) are also used in\nabbreviations. Similarly, colons can be used in chemical names. But the every language comes in\nwith different abbreviations that need to be recognized.</p>\n\n<p>Currently, some abbreviations are found in <a href=\"https://bitbucket.org/wwmm/oscar4/src/005ffa00a69d/oscar4-core/src/main/java/uk/ac/cam/ch/wwmm/oscar/document/NonSentenceEndings.java\">NonSentenceEndings</a>.\nIn the past three months, we have been cleaning up the code, and restructured the source code,\nmaking it easier to detect such places. This class will likely undergo further refactoring, to\nmaking the list of such non-sentence-endings configurable via files or so. What I expect to see,\nis that we you initiate Oscar like this:</p>\n\n<div class=\"language-java highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"nc\">Oscar</span> <span class=\"n\">oscar</span> <span class=\"o\">=</span> <span class=\"k\">new</span> <span class=\"nc\">Oscar</span><span class=\"o\">(</span><span class=\"nc\">Locale</span><span class=\"o\">.</span><span class=\"na\">US</span><span class=\"o\">);</span>\n</code></pre></div></div>\n\n<p>This might actually even make a nice student summer project. The biggest challenge will be in making a good\ncorpus of training data, like the SciBorg training data that was used for training Oscar3.</p>\n\n<p>But the whole normalization is tainted with English language specifics too. For example, the normalizer\nwill have to ‘normalize’ the question marks, for which there exist several\n<a href=\"http://en.wikipedia.org/wiki/Question_mark#Stylistic_variants\">unicode variations</a>.\nBut the normalized variant is language dependent. For example, greek and armenian have different characters\n(see <a href=\"http://en.wikipedia.org/wiki/Question_mark#Opening_and_closing_question_marks\">this page</a>),\nand then we have not even started talking about the right to left.</p>\n\n<p>Besides localized dictionaries, this Oscar will also benefit from a localized <a href=\"http://opsin.ch.cam.ac.uk/\">OPSIN</a>.\nIt seem to recognize the Dutch <a href=\"https://opsin.ch.cam.ac.uk/opsin/propaan.png\">propaan</a>, but not\n<a href=\"https://opsin.ch.cam.ac.uk/opsin/benzeen.png\">benzeen</a>. I am not going to look at that soon, but if you are\ninterested, I recommend checking out Rich’\n<a href=\"https://doi.org/10.59350/bbrwt-e5n35\">posts <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\n<a href=\"https://doi.org/10.59350/vtadn-tdt17\">about <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\n<a href=\"https://doi.org/10.59350/nbtxd-kdz73\">forking <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\nOPSIN and writing patches.</p>\n\n<p>Getting Oscar going for other languages is a challenge, but also offers new opportunities. Just email the\n<a href=\"http://sourceforge.net/mailarchive/forum.php?forum_name=oscar3-chem-developers\">oscar mailing list</a>\nif you are interested and need help.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Apodaca, R. (2010). Open Source Name To Structure Conversion of IUPAC Nomenclature - OPSIN Revisited. In <i>Front Matter</i>. Front Matter. https://doi.org/10.59350/nbtxd-kdz73 <a href=\"https://doi.org/10.59350/nbtxd-kdz73\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.59350/nbtxd-kdz73\">Scholia</a></div>\n    <div class=\"csl-entry\">Apodaca, R. (2010). Plugging Into OPSIN - How to Synchronize Git and Mercurial Repositories. In <i>Front Matter</i>. Front Matter. https://doi.org/10.59350/vtadn-tdt17 <a href=\"https://doi.org/10.59350/vtadn-tdt17\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.59350/vtadn-tdt17\">Scholia</a></div>\n    <div class=\"csl-entry\">Apodaca, R. (2010). Working With OPSIN - Using Netbeans for a Maven Project. In <i>Front Matter</i>. Front Matter. https://doi.org/10.59350/bbrwt-e5n35 <a href=\"https://doi.org/10.59350/bbrwt-e5n35\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.59350/bbrwt-e5n35\">Scholia</a></div>\n  </div>",
      "summary": "Oscar is a text miner. It mines in text for chemistry. Oscar4 is the next iteration of Oscar code that I worked on in the past three months, with Lezan, Sam, and David. I blogged about aspects of Oscar4 at several occasions:",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/c2w.png",
      "date_published": "2010-12-30T00:00:00+00:00",
      "date_modified": "2026-05-05T00:00:00+00:00",
      "tags": ["oscar","textmining"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.59350/vtadn-tdt17", "doi": "10.59350/vtadn-tdt17"
             }
            ,
          
        
          
          
            { "url": "https://doi.org/10.59350/nbtxd-kdz73", "doi": "10.59350/nbtxd-kdz73"
             }
            ,
          
        
          
          
            { "url": "https://doi.org/10.59350/bbrwt-e5n35", "doi": "10.59350/bbrwt-e5n35"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}
