{
  "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/2010/03/22/oxford-august-2010-echeminfo-predictive.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/10.59350/46jj1-62e14",
      "url": "https://chem-bla-ics.linkedchemistry.info/2010/03/22/oxford-august-2010-echeminfo-predictive.html",
      "title": "Oxford, August 2010: eCheminfo Predictive ADME & Toxicology 2010 Workshop",
      "content_html": "<p>The first week of August I will attend the <a href=\"http://echeminfo.com/COMTY_oxfordadmet10\">eCheminfo Predictive ADME &amp; Toxicology Workshop</a>\n(<a href=\"http://events.linkedin.com/eCheminfo-Predictive-ADME-Toxicology/pub/271590\">LinkedIn Event</a>) for which I received a\n<a href=\"http://barryhardy.blogs.com/cheminfostream/2010/02/bursary-award-applications-echeminfo-oxford-2010-workshops.html\">Bursary Award</a>.\nIt will be my first time in Oxford, and I am very much looking forward to it!</p>\n\n<p>The meeting is also bound to be fun. I have not done much in the area of toxicology other than the more general QSAR/QSPR model\nbuilding with chemometrics. But I have been recently taking to Nina and other of the <a href=\"http://www.opentox.org/\">OpenTox</a> community,\nand started to play a bit with the data and computation API they are developing.</p>\n\n<p><img src=\"/assets/images/bioclipseOpenTox.png\" alt=\"\" /></p>\n\n<p>I started a Bioclipse plugin recently (see screenshot), and placed the source code in <a href=\"http://gitorious.org/bioclipse-opentox/bioclipse-opentox\">this bioclipse-opentox</a>\nGit repository on <a href=\"http://gitorious.org/\">Gitorious</a> (<a href=\"http://github.com/egonw\">my GitHub account</a> is already over the formal limit).\nThe functionality is still quite limited, and the manager currently only provides methods to download data sets\n(<a href=\"http://www.myexperiment.org/workflows/1192\">myexperiment:1192</a>):</p>\n\n<div class=\"language-javascript highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"c1\">// query a service using the OpenTox API 1.1</span>\n<span class=\"c1\">// See: http://www.opentox.org/dev/apis/api-1.1</span>\n\n<span class=\"kd\">var</span> <span class=\"nx\">service</span> <span class=\"o\">=</span> <span class=\"dl\">\"</span><span class=\"s2\">http://apps.ideaconsult.net:8180/ambit2/</span><span class=\"dl\">\"</span><span class=\"p\">;</span>\n\n<span class=\"kd\">var</span> <span class=\"nx\">datasets</span> <span class=\"o\">=</span> <span class=\"nx\">opentox</span><span class=\"p\">.</span><span class=\"nf\">listDataSets</span><span class=\"p\">(</span><span class=\"nx\">service</span><span class=\"p\">);</span>\n<span class=\"k\">for </span><span class=\"p\">(</span><span class=\"kd\">set</span><span class=\"o\">=</span><span class=\"mi\">0</span><span class=\"p\">;</span> <span class=\"kd\">set</span><span class=\"o\">&lt;</span><span class=\"nx\">datasets</span><span class=\"p\">.</span><span class=\"nf\">size</span><span class=\"p\">();</span> <span class=\"kd\">set</span><span class=\"o\">++</span><span class=\"p\">)</span> <span class=\"p\">{</span>\n  <span class=\"kd\">var</span> <span class=\"nx\">dataset</span> <span class=\"o\">=</span> <span class=\"nx\">datasets</span><span class=\"p\">.</span><span class=\"nf\">get</span><span class=\"p\">(</span><span class=\"kd\">set</span><span class=\"p\">);</span>\n  <span class=\"nx\">js</span><span class=\"p\">.</span><span class=\"nf\">say</span><span class=\"p\">(</span><span class=\"dl\">\"</span><span class=\"s2\">Downloading set: </span><span class=\"dl\">\"</span> <span class=\"o\">+</span> <span class=\"nx\">dataset</span><span class=\"p\">);</span>\n  <span class=\"nx\">ui</span><span class=\"p\">.</span><span class=\"nf\">open</span><span class=\"p\">(</span>\n    <span class=\"nx\">opentox</span><span class=\"p\">.</span><span class=\"nf\">downloadDataSetAsMDLSDfile</span><span class=\"p\">(</span>\n       <span class=\"nx\">service</span><span class=\"p\">,</span> <span class=\"nx\">dataset</span><span class=\"p\">,</span> <span class=\"dl\">\"</span><span class=\"s2\">/OpenTox/ambit</span><span class=\"dl\">\"</span> <span class=\"o\">+</span> <span class=\"nx\">dataset</span> <span class=\"o\">+</span> <span class=\"dl\">\"</span><span class=\"s2\">.sdf</span><span class=\"dl\">\"</span>\n    <span class=\"p\">)</span>\n  <span class=\"p\">)</span>\n<span class=\"p\">}</span>\n</code></pre></div></div>\n\n<p>Behind this plugin is again the RDF plugin, as OpenTox uses RDF too, a few simple SPARQL queries was all that needed to be defined.\nAnd <a href=\"https://chem-bla-ics.linkedchemistry.info/2010/03/15/rdf-powered-qsar-wizard-sparql-end.html\">again <i class=\"fa-solid fa-recycle fa-xs\"></i></a>, the Bioclipse pluigin\ncode base is pretty small.</p>",
      "summary": "The first week of August I will attend the eCheminfo Predictive ADME &amp; Toxicology Workshop (LinkedIn Event) for which I received a Bursary Award. It will be my first time in Oxford, and I am very much looking forward to it!",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/bioclipseOpenTox.png",
      "date_published": "2010-03-22T00:00:00+00:00",
      "date_modified": "2026-09-27T00:00:00+00:00",
      "tags": ["bioclipse","qsar","toxicology","opentox","ambit"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}