What can Bioinformaticians learn from YouTube?

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A critical look at what those involved in providing bioinformatics tools and data can learn from YouTube.

Published in: Technology, Design

What can Bioinformaticians learn from YouTube?

  1. 1. What can Bioinformaticians learn from YouTube?
  2. 2. Data
  3. 3. New project. New schema.
  4. 4. EMBL: 20 different data formats
  5. 5. “A biologist would rather share their toothbrush than their (gene) names” Mike Ashburner
  6. 6. YouTube loves to share
  7. 7. 100 million views per day
  8. 8. 114 apps
  9. 9. <rdf:RDF xmlns=quot;http://www.affymetrix.com/community/ publications/affymetrix/tmsplice#quot;
  10. 10. <Gene rdf:about=quot;#1110002A21Rikquot;> <chr>chr1</chr> <hasVariant rdf:parseType=quot;Resourcequot;> <representedBy rdf:resource=quot;#gi13385627quot;/> </hasVariant> <hasVariant rdf:parseType=quot;Resourcequot;> <representedBy rdf:resource=quot;#gi18043402quot;/> </hasVariant> <strand>+</strand> </Gene>
  11. 11. RDF, OWL, SPARQL, GRDDL, WTF?
  12. 12. Lower case ‘s’, lower case ‘w’ The semantic web, not The Semantic Web
  13. 13. <tr> <th class=quot;two-columnquot;>Gene</th> <td class=quot;two-columnquot;><table width=quot;100%quot; cellpadding=quot;4quot;> <tr> <td><strong> <a href=quot;http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/ get_data.pl?hgnc_id=1101quot;>BRCA2</a></div></strong> (HGNC Symbol) </td> <td> <span class=quot;smallquot;> To view all Ensembl genes linked to the name <a href=quot;/Homo_sapiens/featureview?type=Gene;id=BRCA2quot;>click here</a>.</span> </td> </tr> </table><p> This gene is a member of the Human CCDS set: <a href=quot;http:// www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi? REQUEST=CCDS&amp;DATA=CCDS9344quot;>CCDS9344</a> </p> </td> </tr>
  14. 14. <tr class=quot;hgenequot;> <th class=quot;two-columnquot;>Gene</th> <td class=quot;two-columnquot;><table width=quot;100%quot; cellpadding=quot;4quot;> <tr> <td><strong> <a href=quot;http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/ get_data.pl?hgnc_id=1101quot; rel=quot;hgnc_namequot;>BRCA2</a></div></strong> (HGNC Symbol) </td> <td> <span class=quot;smallquot;> To view all Ensembl genes linked to the name <a href=quot;/Homo_sapiens/featureview?type=Gene;id=BRCA2quot; rel=quot;gene_listquot; >click here</a>.</span> </td> </tr> </table><p> This gene is a member of the Human CCDS set: <a href=quot;http:// www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi? REQUEST=CCDS&amp;DATA=CCDS9344quot; rel=quot;ccdsquot;>CCDS9344</a> </p> </td> </tr>
  15. 15. Can our web site be our API?
  16. 16. http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618
  17. 17. 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' );
  18. 18. More data on our sites than through the API (we’re not the only ones)
  19. 19. RSS
  20. 20. iCal
  21. 21. XML
  22. 22. ational state Represent transfer RESTful service
  23. 23. psd-production/projects
  24. 24. GET psd-production/projects RETRIEVE
  25. 25. <projects>

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