{
  "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/2009/10/15/sparql-end-points-jena-and-bifcontains.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/g7yhg-frs33",
      "url": "https://chem-bla-ics.linkedchemistry.info/2009/10/15/sparql-end-points-jena-and-bifcontains.html",
      "title": "SPARQL end points, Jena and bif:contains",
      "content_html": "<p>I have been having fun with SPARQL in <a href=\"http://www.bioclipse.net/\">Bioclipse</a> for a while now, and blogged at several occasions:</p>\n\n<ul>\n  <li><a href=\"\">NMRShiftDB enters rdf.openmolecules.net #2: SPARQL end point with Virtuoso</a></li>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2009/08/21/bioclipse-and-sparql-end-points-2.html\">Bioclipse and SPARQL end points #2: MyExperiment <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n  <li><a href=\"https://chem-bla-ics.linkedchemistry.info/2009/08/16/bioclipse-and-sparql-end-points.html\">Bioclipse and SPARQL end points <i class=\"fa-solid fa-recycle fa-xs\"></i></a></li>\n</ul>\n\n<p>One thing I had not been able to work out, is that <a href=\"http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/\">Virtuoso</a> uses a\n(rather nice) <em>bif:contains</em> extension that support indexing. However, <a href=\"http://jena.sourceforge.net/\">Jena</a> would complain with:</p>\n\n<div class=\"language-plaintext highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>com.hp.hpl.jena.query.QueryParseException: Line 1, column 31: Unresolved\nprefixed name: bif:contains\n</code></pre></div></div>\n\n<p>Defining the prefix did not solve the problem either, but <a href=\"http://www.linkedin.com/in/ivanmikhailov\">Ivan Mikhailov</a> just\nreplied to my post to the <a href=\"https://sourceforge.net/mailarchive/forum.php?forum_name=virtuoso-users\">virtuoso-user</a> mailing\nlist providing the solution.</p>\n\n<p>The solution is in the fact that <code class=\"language-plaintext highlighter-rouge\">bif:</code> is in its own namespace, which makes it possible to replace <code class=\"language-plaintext highlighter-rouge\">bif:contains</code> by its\nfull reference <code class=\"language-plaintext highlighter-rouge\">&lt;bif:contains&gt;</code>. I directly gave that a try in Bioclipse, and just succesfull ran this Bioclipse\nscript snippet:</p>\n\n<div class=\"language-javascript highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"nx\">rdf</span><span class=\"p\">.</span><span class=\"nf\">sparqlRemote</span><span class=\"p\">(</span>\n  <span class=\"dl\">\"</span><span class=\"s2\">http://bio2rdf.org/sparql</span><span class=\"dl\">\"</span><span class=\"p\">,</span>\n  <span class=\"dl\">\"</span><span class=\"s2\">SELECT * WHERE {?s ?p ?o . ?o &lt;bif:contains&gt; </span><span class=\"se\">\\\"</span><span class=\"s2\">aspirin</span><span class=\"se\">\\\"</span><span class=\"s2\"> .};</span><span class=\"dl\">\"</span>\n<span class=\"p\">);</span>\n</code></pre></div></div>\n\n<p>Thanx, Ivan!</p>",
      "summary": "I have been having fun with SPARQL in Bioclipse for a while now, and blogged at several occasions:",
      
      "date_published": "2009-10-15T00:00:00+00:00",
      "date_modified": "2026-03-19T00:00:00+00:00",
      "tags": ["sparql","rdf","bioclipse","bio2rdf"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}