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<h1>Taxonomic Search Engine - LSID</h1>
<h2>Federating taxonomic databases using web services</h2>
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<h2>What are they?</h2>
<p><strong>L</strong>ife <strong>S</strong>cience <strong>Id</strong>entifiers. 
  They are a uniform way to name and locate pieces of information on the web. Essentially, 
  an LSID is a unique identifier for some data, and the LSID protocol specifies 
  a standard way to locate the data (as well as a standard way of describing that 
  data). They are a little like <a href="http://www.doi.org/" target="_blank">DOI</a>s used by 
  many publishers. For details see <a href="http://www-124.ibm.com/developerworks/oss/lsid/" target="_blank">IBM's 
  LSID Project</a> and<a href="http://www.i3c.org/"> I3C</a>. There is a lot of 
  interest in LSIDs in both the bioinformatics and the biodiversity communities.</p>
<h2>Why does TSE use them?</h2>

<p>I'm experimenting with how useful LSIDs would be as a means to assign a unique 
  identifier to a taxonomic name/concept. The idea is that a database that needed 
  to store taxonomic information would need only store a LSID. Another nice feature 
  of LSIDs is that they can be resolved to metada, that is, given a LSID you can 
  retrieve a <a href="http://www.w3.org/RDF/" target="_blank">RDF</a> document with details about the object the LSID points to. If 
  we view taxonomic names as metadata, then this is, in fact, all we need. If 
  there is a standard RDF format for taxonomic metadata then a client database 
  needs only one bit of code to make sense of the information from any taxonomic 
  database that it relies on.</p>
  
<h2>RDF</h2>
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 <td>
<p>Resource Description Framework (RDF) is a standard promoted by <a href="http://www.w3.org/">W3C</a>.
For an introduction see Tim Bray's article <a href="http://www.xml.com/pub/a/2001/01/24/rdf.html">What is RDF?</a>. 
W3C provide a very useful <a href="http://www.w3.org/RDF/Validator/" target="_blank">RDF Validation Service</a> complete with 
(optional) graphical output.</p>
<p>You can view the <a href="http://itis.usda.gov.lsid.zoology.gla.ac.uk/authority/metadata/?lsid=urn:lsid:itis.usda.gov.lsid.zoology.gla.ac.uk:tsn:180092" target="_blank">
RDF associated with the LSID for the ITIS record for <i>Homo sapiens</i></a>.</p>
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<td><a href="http://www.w3.org/RDF/" title="RDF Resource Description
Framework"> <img border="0" src="http://www.w3.org/RDF/icons/rdf_w3c_icon.48"
alt="RDF Resource Description Framework Icon"></a></td>
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</table>

<h2>How does one look at them?</h2>
<p>To make use of LSIDs you need software that can resolve them. If you are a 
  programmer, then <a href="http://www-124.ibm.com/developerworks/oss/lsid/">IBM's 
  LSID Project</a> provides code and examples for Perl and Java. If you want a 
  simple client, then there are three options.</p>
<h3>1. LSID Launchpad</h3>
<table border="0">
  <tr>
    <td><img src="images/launchpad_small.gif"></td>
    <td valign="top"><p>LSID Launchpad is available free from IBM and requires 
        Windows 2000/XP and Internet Explorer 6 (no other browser will work). You 
        can get it from <a href="http://www-124.ibm.com/developerworks/oss/lsid/" target="_blank">IBM's 
        LSID Project</a> site.</p>
      <p>A good way to check whether Lauchpad is working is to go to the <a href="http://lsid.limnology.wisc.edu/" target="_blank">North 
        Temperate Lakes - LTER LSID authority page</a> and try their LSIDs.</p>
      <p>Once installed, you should be able to resolve a LSID served up by TSE, 
        such as <a href="lsidres:urn:lsid:itis.usda.gov.lsid.zoology.gla.ac.uk:tsn:178010">urn:lsid:itis.usda.gov.lsid.zoology.gla.ac.uk:tsn:178010</a> 
        . If this doesn't work, you may have to tell LSID Launchpad where to look 
        for the resolver. For the LSID above, click on the &quot;Configure&quot; 
        link at the top right of the Launchpad window, click on the &quot;Edit 
        authorities...&quot; button, and add the following:</p>
      <table border="0" cellpadding="2" cellspacing="2">
        <tr>
          <td><strong>Authority</strong></td>
          <td>itis.usda.gov.lsid.zoology.gla.ac.uk</td>
        </tr>
        <tr>
          <td><strong>Address</strong></td>
          <td>http://itis.usda.gov.lsid.zoology.gla.ac.uk:80/authority</td>
        </tr>
      </table>
      <p>This should now resolve the LSID, and you should see a simple report 
        for the taxon (in this example, <em>Apus</em> <em>apus</em>).</p>
      </td>
  </tr>
</table>
<h3>2. Biopathways Consortium LSID Resolver</h3>
<p>The Biopathways Consortium provide a <a href="http://biopathways.ibm.nebiogrid.org/webresolver/" target="_blank">web 
  LSID resolver</a> that can be used on any platform. You can paste in a LSID and you get back the metadata. You 
  can also create a URL with an LSID, for example </p>
<p><a href="http://biopathways.ibm.nebiogrid.org/resolver/urn:lsid:itis.usda.gov.lsid.zoology.gla.ac.uk:tsn:180092" target="_blank">http://biopathways.ibm.nebiogrid.org/resolver/urn:lsid:itis.usda.gov.lsid.zoology.gla.ac.uk:tsn:180092</a></p>
<p>Clicking on this link takes you directly to the result of resolving the LSID.</p>

<h3>3. LSID extension for Mozilla/Firefox</h3>
<p>If you use Mozilla or Firefox you can install my <a href="http://lsid.mozdev.org/" target="_blank">LSID extension</a> which makes LSIDs prefixed with the <tt>lsidres</tt> protocol
such as <a href="lsidres:urn:lsid:itis.usda.gov.lsid.zoology.gla.ac.uk:tsn:178010">urn:lsid:itis.usda.gov.lsid.zoology.gla.ac.uk:tsn:178010</a> 
clickable. This extension should work on any platform for which Firefox is available.</p>

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