<html>
<head>
<title>Taxonomic Search Engine</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<link rel="stylesheet" href="portal.css" type="text/css" media="screen" />
</head>
<body>
<h1>Taxonomic Search Engine - LSID</h1>
<h2>Federating taxonomic databases using web services</h2>
<?php include("top.inc.php"); ?>
<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>
<table border="0">
<tr>
<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>
</td>
<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>
</tr>
</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 "Configure"
link at the top right of the Launchpad window, click on the "Edit
authorities..." 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>
</body>
</html>