{
  "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/2010/10/21/oscar-text-mining-in-taverna.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/10.59350/7njvw-s6q24",
      "url": "https://chem-bla-ics.linkedchemistry.info/2010/10/21/oscar-text-mining-in-taverna.html",
      "title": "Oscar text mining in Taverna",
      "content_html": "<p>One of the goals of my <a href=\"https://chem-bla-ics.linkedchemistry.info/2010/10/15/working-on-oscar-for-three-months.html\">project in Cambridge <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\nis to make <a href=\"http://oscar3-chem.sourceforge.net/\">Oscar</a> available as <a href=\"http://taverna.sf.net/\">Taverna</a> plugin\n(<a href=\"https://bitbucket.org/egonw/oscar4-taverna\">source code</a>, <a href=\"https://hudson.ch.cam.ac.uk/job/oscar4-taverna/\">Hudson build</a>).\nI have progressed somewhat, but still struggling with getting the update site working. The plugin actually installs into\n<a href=\"http://www.mygrid.org.uk/2010/07/taverna-220-workbench-and-command-line-tool-are-released/\">Taverna 2.2.0</a>, but the\nactivities do not show up. While this is work in progress, and the other project goal is refactoring, a current demo\nworkflow looks like:</p>\n\n<p><img src=\"/assets/images/oscarTaverna.png\" alt=\"\" /></p>\n\n<p>Example input would be: <em>This is a list of ethanol, methanol, and 2,4,6-trinitrotoluene.</em></p>\n\n<p>The plain text input can be linked to the pdf2text <a href=\"http://www.slideshare.net/markmoby/sadi-in-taverna-tutorial\">SADI service</a>,\nand the CML is suitable for the <a href=\"https://chem-bla-ics.linkedchemistry.info/2010/03/29/cdk-taverna-paper-published.html\">CDK-Taverna plugin <i class=\"fa-solid fa-recycle fa-xs\"></i></a>,\nwhich is currently being updated by Andreas, Achim, and <a href=\"http://www.steinbeck-molecular.de/steinblog/\">Christoph</a> for\nTaverna 2.2. As soon as the update site is properly working, I will upload a demo workflow to\n<a href=\"http://www.myexperiment.org/\">MyExperiment.org</a>.</p>\n\n<p>I guess the first next activity (node in the workflow) will be around the dictionaries, as the\n<a href=\"http://opsin.ch.cam.ac.uk/\">OPSIN</a> activity converts only IUPAC names into connection tables. I was told OPSIN parses 97%\nof the IUPAC names it finds, and when it does, it does almost 100% correct. Want to challenge the code?\nUse <a href=\"http://opsin.ch.cam.ac.uk/\">this web service</a>.</p>",
      "summary": "One of the goals of my project in Cambridge is to make Oscar available as Taverna plugin (source code, Hudson build). I have progressed somewhat, but still struggling with getting the update site working. The plugin actually installs into Taverna 2.2.0, but the activities do not show up. While this is work in progress, and the other project goal is refactoring, a current demo workflow looks like:",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/oscarTaverna.png",
      "date_published": "2010-10-21T00:00:00+00:00",
      "date_modified": "2026-09-27T00:00:00+00:00",
      "tags": ["oscar","taverna"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}