Introduction to the Semantic Web

Slide 2: “ 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

Slide 3: “ AWESOME ” Me, just now

Slide 4: “ 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

Slide 5: Documents vs Data

Slide 6: XML and URI Uniform resource identifiers and namespaces

Slide 7: <rdf:RDF xmlns="http://www.affymetrix.com/community/ publications/affymetrix/tmsplice#"

Slide 9: RDF and OWL Resource Description Format and the Web Ontology Language

Slide 10: <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>

Slide 11: <Exon rdf:about="#1110002A21Rik_e3"> <commonToAll>1</commonToAll> <startsAt>37936751</startsAt> <stopsAt>37937035</stopsAt> </Exon>

Slide 12: <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>

Slide 13: RDF Schema Formal XML definition for an RDF file

Slide 14: SPARQL Standard RDF query language

Slide 15: WTF?

Slide 16: too ambitious?

Slide 17: let’s go with what works now

Slide 18: lower case ‘s’, lower case ‘w’ The semantic web, not The Semantic Web

Slide 19: Add semantic value to data in existing documents

Slide 20: <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>

Slide 21: <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>

Slide 22: 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

Slide 23: Style it. Parse it.

Slide 24: Can our website be our API?

Slide 25: http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618

Slide 26: 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' );

Slide 27: More data on the web than from the API (we’re not the only ones)

Slide 29: wikipedia.org/wiki/Semantic_Web wikipedia.org/wiki/Namespace wikipedia.org/wiki/Web_Ontology_Language

Slide 30: microformats.org

Slide 31: bioformats.org

Slide 32: slideshare.net/mza