{
  "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/2011/09/27/almost-year-ago-i-started-position-with.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/qgrq1-4r761",
      "url": "https://chem-bla-ics.linkedchemistry.info/2011/09/27/almost-year-ago-i-started-position-with.html",
      "title": "Bioclipse-Oscar4 - Text mining in Bioclipse",
      "content_html": "<p>Almost a year ago I <a href=\"https://chem-bla-ics.linkedchemistry.info/2010/10/15/working-on-oscar-for-three-months.html\">started a position <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\nwith <a href=\"http://blogs.ch.cam.ac.uk/pmr/\">Peter Murray-Rust</a> to work on Oscar for three months (see this overview of results;\na paper by the full Oscar team (Sam, David, Dan, Lezan) is pending, and I’m really happy to have been able to contribute\nbits to the project). Since then, I have had little time :( That’s how it goes, with post-hopping, unfortunately.\nOne thing I did do after that, was write a <a href=\"https://github.com/bioclipse/bioclipse.oscar\">Bioclipse plugin</a>.</p>\n\n<p>I was asked recently via <a href=\"http://www.linkedin.com/in/egonw\">LinkedIn</a> if I was planning a Bioclipse-Oscar plugin, and\nI realized that I forgot to blog about it. So, here goes. The <code class=\"language-plaintext highlighter-rouge\">oscar</code> manager I implemented follows the\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2010/10/28/oscar4-java-api-chemical-name.html\">Oscar API <i class=\"fa-solid fa-recycle fa-xs\"></i></a>, and these\nmethods are available: <code class=\"language-plaintext highlighter-rouge\">extractText()</code>, <code class=\"language-plaintext highlighter-rouge\">findNamedEntities()</code>,  <code class=\"language-plaintext highlighter-rouge\">findResolvedNamedEntities()</code>.</p>\n\n<p>When I wrote the plugin, I also uploaded an <a href=\"http://www.myexperiment.org/workflows/2117.html\">example workflow to MyExperiment</a>.\nThe code is:</p>\n\n<div class=\"language-javascript highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"c1\">// Demo showing the Oscar text mining functionality</span>\n<span class=\"c1\">// in Bioclipse</span>\n<span class=\"kd\">var</span> <span class=\"nx\">html</span> <span class=\"o\">=</span> <span class=\"nx\">bioclipse</span><span class=\"p\">.</span><span class=\"nf\">download</span><span class=\"p\">(</span>\n  <span class=\"dl\">\"</span><span class=\"s2\">http://dx.doi.org/10.3762/bjoc.6.133</span><span class=\"dl\">\"</span><span class=\"p\">,</span>\n  <span class=\"dl\">\"</span><span class=\"s2\">text/html</span><span class=\"dl\">\"</span>\n<span class=\"p\">)</span>\n<span class=\"kd\">var</span> <span class=\"nx\">text</span> <span class=\"o\">=</span> <span class=\"nx\">oscar</span><span class=\"p\">.</span><span class=\"nf\">extractText</span><span class=\"p\">(</span><span class=\"nx\">html</span><span class=\"p\">);</span>\n<span class=\"c1\">// the next step may take some time, while</span>\n<span class=\"c1\">// initializing the Oscar software for the</span>\n<span class=\"c1\">// first time</span>\n<span class=\"kd\">var</span> <span class=\"nx\">mols</span> <span class=\"o\">=</span> <span class=\"nx\">oscar</span><span class=\"p\">.</span><span class=\"nf\">findResolvedNamedEntities</span><span class=\"p\">(</span><span class=\"nx\">text</span><span class=\"p\">);</span>\n<span class=\"kd\">var</span> <span class=\"nx\">file</span> <span class=\"o\">=</span> <span class=\"dl\">\"</span><span class=\"s2\">/Oscar Demo/extractedMols.sdf</span><span class=\"dl\">\"</span><span class=\"p\">;</span>\n<span class=\"nx\">cdk</span><span class=\"p\">.</span><span class=\"nf\">saveSDFile</span><span class=\"p\">(</span><span class=\"nx\">file</span><span class=\"p\">,</span> <span class=\"nx\">mols</span><span class=\"p\">);</span>\n<span class=\"nx\">ui</span><span class=\"p\">.</span><span class=\"nf\">open</span><span class=\"p\">(</span><span class=\"nx\">file</span><span class=\"p\">);</span>\n</code></pre></div></div>\n\n<p>The code will extract chemical entities, and open a molecules table in <a href=\"http://www.bioclipse.net/\">Bioclipse</a>:</p>\n\n<p><img src=\"/assets/images/oscarDemo2.png\" alt=\"\" /></p>",
      "summary": "Almost a year ago I started a position with Peter Murray-Rust to work on Oscar for three months (see this overview of results; a paper by the full Oscar team (Sam, David, Dan, Lezan) is pending, and I’m really happy to have been able to contribute bits to the project). Since then, I have had little time :( That’s how it goes, with post-hopping, unfortunately. One thing I did do after that, was write a Bioclipse plugin.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/oscarDemo2.png",
      "date_published": "2011-09-27T00:00:00+00:00",
      "date_modified": "2025-03-05T00:00:00+00:00",
      "tags": ["oscar","bioclipse","beilstein"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}