“ The Semantic Web is not a separate Web but an
extension of the current one, in which information is
given well-defined meaning, better enabling
”
computers and people to work in cooperation
Sir Tim, 2002

“ AWESOME
”
Me, just now

“ The Semantic Web is not a separate Web but an
extension of the current one, in which information is
given well-defined meaning, better enabling
”
computers and people to work in cooperation
Sir Tim, 2002
not quite true

Documents vs Data

XML and URI
Uniform resource identifiers and namespaces

<rdf:RDF xmlns="http://www.affymetrix.com/community/
publications/affymetrix/tmsplice#"

RDF and OWL
Resource Description Format and the
Web Ontology Language

<Gene rdf:about="#1110002A21Rik">
<chr>chr1</chr>
<hasVariant rdf:parseType="Resource">
<representedBy rdf:resource="#gi13385627"/>
</hasVariant>
<hasVariant rdf:parseType="Resource">
<representedBy rdf:resource="#gi18043402"/>
</hasVariant>
<strand>+</strand>
</Gene>

<Exon rdf:about="#1110002A21Rik_e3">
<commonToAll>1</commonToAll>
<startsAt>37936751</startsAt>
<stopsAt>37937035</stopsAt>
</Exon>

<Transcript rdf:about="#gi13385627">
<hasCds rdf:parseType="Resource">
<startsAt>37936755</startsAt>
<stopsAt>37944277</stopsAt>
</hasCds>
<hasExon rdf:parseType="Resource">
<cdsType>None</cdsType>
<relatesToExon rdf:resource="#1110002A21Rik_e3"/>
</hasExon>
...
</Transcript>

RDF Schema
Formal XML definition for an RDF file

SPARQL
Standard RDF query language

WTF?

too ambitious?

let’s go with what
works now

lower case ‘s’, lower case ‘w’
The semantic web, not
The Semantic Web

Add semantic value to data
in existing documents

<tr>
<th class="two-column">Gene</th>
<td class="two-column"><table width="100%" cellpadding="4">
<tr>
<td><strong>
<a href="http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/
get_data.pl?hgnc_id=1101">BRCA2</a></div></strong> (HGNC
Symbol)
</td>
<td>
<span class="small"> To view all Ensembl genes linked to the
name <a href="/Homo_sapiens/featureview?
type=Gene;id=BRCA2">click here</a>.</span>
</td>
</tr>
</table><p>
This gene is a member of the Human CCDS set: <a href="http://
www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?
REQUEST=CCDS&amp;DATA=CCDS9344">CCDS9344</a>
</p>
</td>
</tr>

<tr class="hgene">
<th class="two-column">Gene</th>
<td class="two-column"><table width="100%" cellpadding="4">
<tr>
<td><strong>
<a href="http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/
get_data.pl?hgnc_id=1101" rel="hgnc_name">BRCA2</a></div></
strong> (HGNC Symbol)
</td>
<td>
<span class="small"> To view all Ensembl genes linked to the
name <a href="/Homo_sapiens/featureview?type=Gene;id=BRCA2"
rel="gene_list" >click here</a>.</span>
</td>
</tr>
</table><p>
This gene is a member of the Human CCDS set: <a href="http://
www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?
REQUEST=CCDS&amp;DATA=CCDS9344" rel="ccds">CCDS9344</a>
</p>
</td>
</tr>

Cool, me too!
I’m going to mark up
genes like this
Cool, me too!
Cool, me too!
Cool, me too!
Cool, me to
Apologies to Dan Cederholm: simplebits.com

Style it. Parse it.

Can our website be our API?

http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618

http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618
my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
my $gene = fetch_by_gene_stable_id( 'ENSG00000139618' );

More data on the web than
from the API
(we’re not the only ones)

wikipedia.org/wiki/Semantic_Web
wikipedia.org/wiki/Namespace
wikipedia.org/wiki/Web_Ontology_Language

microformats.org

bioformats.org

slideshare.net/mza