lifesci.html 8.96 KB

Raw Blame History Permalink

<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta name="generator"
content="HTML Tidy for Mac OS X (vers 1st September 2004), see www.w3.org" />
<meta http-equiv="Content-Type"
content="text/html; charset=us-ascii" />
<title>Semantic Web Advanced Development for Europe
(SWAD-Europe)</title>
<link href="http://www.w3.org/2001/sw/Europe/style/swad-europe-showcase.css"
rel="stylesheet" type="text/css" />
<style type="text/css">/*
<![CDATA[*/

body {
  font-family: verdana, helvetica, arial, sans-serif;
}

#leftcontent {
position: absolute;
left:10px;
top:20px;
width:200px;
        background:#fff;
        margin-right:15px;
        padding-bottom:20px;
}

#rightcontent {
        position: absolute;
                left:250px;
                top:20px;
                background:#fff;

  padding-right: 50px;
}

#mainMenu {
  background-color: #EEE;
  border: 1px solid #CCC;
  color: #000;
  width: 203px;
}

#menuList {
  margin: 0px;
  padding: 10px 0px 10px 15px;
}


li.menubar {
  background: url(http://www.w3.org/2001/sw/Europe/showcase/square.gif) no-repeat 0em 0.3em;
  line-height: 1.5em;
  list-style: none outside;
  font-size: 12px;
}

li.nonexpandingmenubar {
  font-size: 12px;
  line-height: 1.5em;
  list-style: none outside;
  padding-left: 20px;
}

.menu {
  margin-left: 15px;
  padding: 0px;
}

.menu li {
  background: url(http://www.w3.org/2001/sw/Europe/showcase/square.gif) no-repeat 0em 0.3em;
  list-style: none outside;
}

a.actuator {
  background-color: transparent;
  color: #000;
  padding-left: 20px;
  text-decoration: none;
  font-weight: bold;
}


.menu li a {
  background-color: transparent;
  color: #000;
  font-size: 12px;
  padding-left: 15px;
}


span.key {
  text-decoration: underline;
}


/*]]>
*/</style>
</head>
<body>
<div id="leftcontent" valign="top">
<div align="center" valign="top">
<a href="http://www.w3.org/2001/sw/Europe">
<img alt="SWAD-Europe"
src="http://www.w3.org/2001/sw/Europe/images/swade100.gif"
height="75" border="0" /></a>
<a href="http://www.cordis.lu/ist/">
<img src="http://www.w3.org/2001/sw/Europe/images/istlogo-thumb.gif"
alt="EU IST logo" height="75" border="0" /></a>
</div>

<div id="mainMenu">
<ul id="menuList">
<li class="nonexpandingmenubar">
<a href="http://www.w3.org/2001/sw/Europe/" id="introMenu"
name="introMenu">Introduction</a>
</li>
<li class="menubar">
<a id="demosMenuActuator" class="actuator" accesskey="d"
name="demosMenuActuator">Demonstrators</a>
<ul id="demosMenu" class="menu">
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/sem-blog.html">
Semantic Blogging</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/sem-portal.html">
Semantic Portals</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/sem-thes.html">
Thesaurus Browser</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/sem-large.html">
Scale Demonstrator</a>
</li>
</ul>
</li>
<li class="menubar">
<a id="themesMenuActuator" class="actuator" accesskey="t"
name="themesMenuActuator">Themes</a>
<ul id="themesMenu" class="menu">
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/gs.html">Getting
Started</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/reports/tools/">Tools</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/digital-libraries.html">
Digital Libraries</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/business-integration.html">
Business Integration</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/images.html">
Image Description</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/reports/community/">
Community Building</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/history.html">
Project History</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/future.html">
Future Directions</a>
</li>
</ul>
</li>
<li class="menubar">
<a id="guideMenuActuator" class="actuator" accesskey="g"
name="guideMenuActuator">Guidelines</a>
<ul id="guideMenu" class="menu">
<!--<li><a href="blank.html">Aerospace</a> stilo*</li>-->
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/lifesci.html">
Life Science</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/guide-for-librarian.html">
Librarian</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/coder.html">
Coder</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/business-guidelines.html">
Business Integration</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/heritage.html">
Heritage</a>
</li>
</ul>
</li>
<li class="menubar">
<a id="resourcesMenuActuator" class="actuator" accesskey="r"
name="resourcesMenuActuator">Resources</a>
<ul id="resourcesMenu" class="menu">
<li>
<a href="http://www.w3.org/2001/sw/Europe/reports/intro.html">
Reports</a>
</li>
<li>
<a href="http://www.w3.org/2001/sw/Europe/showcase/presentations.html">
Presentations</a>
</li>
</ul>
</li>
<li class="nonexpandingmenubar">
<a href="http://www.w3.org/2001/sw/Europe/showcase/contact.html"
id="contactMenu" name="contactMenu">Contact</a>
</li>
</ul>
</div>
</div>

<!-- content goes here -->
<div id="rightcontent">
<h1 class="title">Guidelines - Life Science</h1>
<h2>Guidelines</h2>
<p>SWAD-Europe guidelines provide pointers into the parts of the
SWAD-Europe project that we feel are particularly relevant to the
concerns of particular industry segments or application area. They
are not intended to be definitive guides to the wider semantic web
resources relevant to the area.</p>
<h2>Semantic Web and life science</h2>
<p>Life science is a very information rich set of activities which
mesh well with the semantic web capabilities.</p>
<p>Firstly, there has been huge effort within life science in
general, and healthcare and drug discovery in particular, to codify
vocabularies, thesauri and ontologies to facilitate information
sharing. Well known examples of these include the <a href=
"http://www.geneontology.org/">Gene Ontology</a>, the <a href=
"http://www.biopax.org/">BioPax</a> molecular pathway ontology, the
<a href="http://ncicb.nci.nih.gov/core/EVS">NCI Cancer Ontology</a>
and the National Library of Medicine <a href=
"http://www.nlm.nih.gov/research/umls/">UMLS</a> metathesaurus (and
associated projects <a href="http://skr.nlm.nih.gov/">SKR</a>). The
semantic web standards for encoding ontologies are very relevant
here and several of these example ontologies are already available
in OWL format.</p>
<p>Secondly, there is huge diversity of information involved in
areas such as drug discovery - genomics, proteomics, protein
structure, molecular pathways, assay results, toxicology, clinical
trial results, peer publications, moderated discussion forums etc.
What's more many of the information sources are often public or
cross organizational leading to a requirement for information
integration and exchange based on open standards. Several
activities are already underway to explore the use of RDF to
facilitate this data exchange and integration. These include
protein sequence data (<a href=
"http://www.isb-sib.ch/%7Eejain/rdf/">UniProt in RDF</a>),
publication information (<a href=
"http://npg.nature.com/npg/servlet/Content?data=xml/02_newsfeed.xml&amp;style=xml/02_newsfeed.xsl">
Nature Publishing Group newsfeed</a>) and identifiers for life
science data objects and concepts (<a href=
"http://www.i3c.org/wgr/ta/resources/lsid/docs/index.asp">LSID</a>).</p>
<p>Thirdly, there are many online services for processing life
science information (such as BLAST services for sequence alignment)
which are being made available as web services. This raises the
question of whether the semantic web can be exploited to describe
these web services to both facilitate discovery and, in the long
term, to enable semiautomatic combination of services. Projects in
this area based on semantic web approaches include <a href=
"http://biomoby.org/">BioMoby</a> and <a href=
"http://www.mygrid.org.uk/">MyGrid</a>.</p>
<p>There has been sufficiently much activity in this area to prompt
W3C to host discussions and workshops specific to applying the
semantic web to life sciences: [<a href=
"http://lists.w3.org/Archives/Public/public-semweb-lifesci/"
target="_top">archives</a>] [<a href=
"http://www.w3.org/2004/07/swls-weblinks.html" target=
"_top">links</a>] [<a href=
"http://www.w3.org/2004/07/swls-cfp.html" target=
"_top">workshop</a>]</p>
<h3>Relevant SWAD-Europe resources</h3>
<p>The key SWAD-Europe themes relevant here are:</p>
<ul>
<li><a href=
"http://www.w3.org/2001/sw/Europe/showcase/digital-libraries.html">The
Digital Library theme</a>, in particular the <a href=
"http://www.w3.org/2001/sw/Europe/reports/thes/">SKOS thesaurus
format</a>, for representation of life science vocabularies.</li>
<li>The <a href=
"http://www.w3.org/2001/sw/Europe/showcase/business-integration.html">
Business Integration theme</a> for resources of relevance to the
data integration problem.</li>
<li>The <a href=
"http://www.w3.org/2001/sw/Europe/reports/tools/">tools page</a>
will be useful for any developer exploring issues such as storage
and query of RDF data in this domain.</li>
</ul>
</div>
</body>
</html>