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BioWikis BSB10

Community annotation and BioWikis by Dan Bolser

Third virtual conference on “Bioinformatics to Systems Biology" Online at Bioinformatics.Org

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BioWikis BSB10

  1. 1. 1 Dan Bolser (dmb@bioinformatics.org) Bioinformatics to Systems Biology October 2010 Community Annotation and BioWikis
  2. 2. 2 Presentation overview  Community annotation  Why is it necessary?  BioWikis  The Wiki Wiki Web!  When does it work?  Game mechanics?
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  4. 4. 4 Community Annotation Has been driven by two key factors:  The vast increase in biological data  The clear success of Wikipedia
  5. 5. 5 BioMoore's Law  Over time: − Cost per unit of information can be decreased by orders of magnitude. − Throughput is increased by orders of magnitude.  Fan et al. 2006. Nat Rev Genet.  Comprehensive disease studies that might require ~1bn genotypes would now cost only a few million dollars. − Revolution in human genetics.
  6. 6. 6 Community Annotation  Centralised databases can't cope with annotating the influx of data.  Less investment in more specialised data.  Fewer people with a stake.  Specialists more disparate. − Communities are smaller and more focused.  Do wikis hold the answer?  Wikipedia as a model…
  7. 7. 7 The Success of Wikipedia  Wikipedia is consistently among one of the top 10 websites in the world (http://www.alexa.com).  Google > Facebook > YouTube > Yahoo! > Windows Live > Baidu > Wikipedia > ...  200k edits per day.  100k active users per month.  WikiProject  Molecular and Cellular Biology
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  9. 9. 9 Why Wikipedia isn’t always the answer • Wikipedia is an educational resource. – All articles are encyclopaedic in style. – Explicitly forbids data from ‘original research’: • http://wikipedia.org/wiki/Wikipedia:No_original_research – Wikipedia does not publish original research. – No tools for analysis, presentation, or collection of ‘biological’ data. • BioWikis!
  10. 10. 10 BioWikis Wikis with a biological subject matter, customized for analysis, presentation and collection of specific biological data and biological data types:
  11. 11. 11 Some examples • WikiPathways – Adds specific pathway creation and editing tools to the wiki. – Data is exported in standard formats via APIs – Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. (2008) WikiPathways: Pathway Editing for the People. PLoS Biol 6(7): doi:10.1371/journal.pbio.0060184 – http://www.wikipathways.org
  12. 12. 12 Some examples • WikiOpener MediaWiki extension – Adds tools like BLAST to the wiki – One of many ‘data extraction extensions’ • http://www.mediawiki.org/wiki/Category:Data_extraction_extensions – Brohée S, Barriot R, Moreau Y. (2010) Biological Wikis: combining wikis with databases. Bioinformatics. 26(17):2210 – http://www.mediawiki.org/wiki/Extension:WikiOpener
  13. 13. 13 Some examples • PDBWiki – Allows the protein structures in the PDB to be tagged with specific annotations. – Functions as a bug tracker for users of the PDB – Stehr H, Duarte JM, Lappe M, Bhak J, Bolser DM. (2010) PDBWiki: added value through community annotation of the Protein Data Bank. Database. baq009 – http://pdbwiki.org
  14. 14. 14 Semantic MediaWiki • Very powerful and generic MediaWiki extension. – Users can contribute structured data via forms using auto-completion. – Contributed data can be visualized in a variety of ways. – Data can be queried and reports produced. • All done within the wiki. • Data is ‘linked’…
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  16. 16. 16 When does it work?
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  18. 18. 18 When does it work?  The barrier to annotation is low.  The annotation provides direct benefit to the user:  Functionality  Self-promotion  Recognition  These factors often depend on COMMUNITY. Infrastructure Ease of use Provenance
  19. 19. 19 Building a community...  Activation energy!  You have to build up a resource before users will contribute!  Kittur et. al. (2007) Power of the few vs. wisdom of the crowd.  http://www.parc.com/publication/ 1749/power-of-the-few-vs- wisdom-of-the-crowd.html
  20. 20. 20 Game mechanics? (Fun) • Crowd sourcing – Using ‘the crowd’ to do useful work • Game mechanics – Applying Game Mechanics to Functional Software – http://www.youtube.com/watch?v=ihUt-163gZI • Ease of use, robust infrastructure, and recognition of user contributions are encapsulated by the simple idea of making the site ‘fun’.
  21. 21. 21 Recognition • People work for recognition. – In science, this typically comes from publication of peer-reviewed papers. – Why contribute to a wiki? • Perhaps this will get you a publication? • Peer review is not just about papers. – Contributors to Wikipedia are recognised among their peers!
  22. 22. 22 Recognition • Alternative models of recognition. – Wiki edits are unlikely to impress anyone on a CV, however… – Community mailing lists are a great way to network. • http://biodatabase.org/index.php/List_of_mailing_lists_for_biologists – Recognition can come from contribution to community projects! • http://bioinformatics.org/wiki !!!
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  24. 24. 24 Conclusions  The wiki concept is a simple improvement on the original concept of the web.  Sharing data.  BioWikis must be fun and attractive for users.  Structured wikis promise to change our idea of a ‘web database’.  Read only databases will be hard to imagine.
  25. 25. 25 Get involved! • BBB mailing list • IRC: – irc://irc.freenode.net/#bioinformatics – irc://irc.freenode.net/#semantic-mediawiki • Wikis! – Wikipedia – Bioinformatics.Org • Email me!
  26. 26. 26 Acknowledgements  Bifx.Org  Directors − Prash, Jeff, ...  All the contributors to http://bifx.org/wiki  Jeff, Cody, D. Hamel, Prash, Sonny, Chris, B Fristensky, Nagpal, Mariap3636, Pingou, ...  Linus Torvalds for Linux, and all scientists who pursue their work with honesty and integrity.  Henning Stehr and Jose Duarte for PDBWiki irc://irc.freenode.net/# bioinformatics
  27. 27. 27 References  Wikinomics: http://www.ncbi.nlm.nih.gov/pubmed/18769412  EcoliWiki / Gene Wiki / OpenWetWare / PDBWiki / Proteopedia / WikiGenes / WikiPathways / …  http://biodatabase.org/index.php/BioWiki  Bioinformatics.Org wiki: http://bifx.org/wiki  The SEQanswers wiki: http://SEQwiki.org  MCB: http://wikipedia.org/wiki/Wikipedia:Project_MCB  BiO Sites: http://BiO.CC
  28. 28. 28 References • See references within: – http://www.ncbi.nlm.nih.gov/pubmed/20624717 – http://www.ncbi.nlm.nih.gov/pubmed/20193066 – http://www.ncbi.nlm.nih.gov/pubmed/18613750 • Semantic MediaWiki: – http://semantic-mediawiki.org – irc://irc.freenode.net/#semantic-mediawiki

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