Introduction to the Semantic Web

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    Introduction to the Semantic Web - Presentation Transcript

    1. “ 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
    2. “ AWESOME ” Me, just now
    3. “ 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
    4. Documents vs Data
    5. XML and URI Uniform resource identifiers and namespaces
    6. <rdf:RDF xmlns="http://www.affymetrix.com/community/ publications/affymetrix/tmsplice#"
    7. RDF and OWL Resource Description Format and the Web Ontology Language
    8. <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>
    9. <Exon rdf:about="#1110002A21Rik_e3"> <commonToAll>1</commonToAll> <startsAt>37936751</startsAt> <stopsAt>37937035</stopsAt> </Exon>
    10. <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>
    11. RDF Schema Formal XML definition for an RDF file
    12. SPARQL Standard RDF query language
    13. WTF?
    14. too ambitious?
    15. let’s go with what works now
    16. lower case ‘s’, lower case ‘w’ The semantic web, not The Semantic Web
    17. Add semantic value to data in existing documents
    18. <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>
    19. <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>
    20. 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
    21. Style it. Parse it.
    22. Can our website be our API?
    23. http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618
    24. 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' );
    25. More data on the web than from the API (we’re not the only ones)
    26. wikipedia.org/wiki/Semantic_Web wikipedia.org/wiki/Namespace wikipedia.org/wiki/Web_Ontology_Language
    27. microformats.org
    28. bioformats.org
    29. slideshare.net/mza

    + Matt WoodMatt Wood, 3 years ago

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