Nice 2012, BioWikis and DASWiki

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Some slides showing some BioWikis developed using Semantic MediaWiki.

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Nice 2012, BioWikis and DASWiki

  1. 1. Some wikis I have known
  2. 2. Some wikis I have known Arguing the case for using 'wiki-style' technology to store structured data by demoing a few of the 'data' wikis that I've created or developed, with an emphasis on wikis for biological data, the so called BioWikis.
  3. 3. My world view...
  4. 4. I WIKI
  5. 5. Disclaimer When I say, "I'm a wiki person" I don't mean to imply that I think wiki is a specific tool that has strengths or weaknesses when compared to another tool, rather I mean that wiki is the realisation of a different philosophy of data curation that I support.
  6. 6. Technology <ul><li>MediaWiki </li><ul><ul><li>...
  7. 7. ... </li></ul></ul></ul><ul><li>Semantic MediaWiki </li><ul><ul><li>...
  8. 8. ... </li></ul></ul></ul>
  9. 9. Wikis!
  10. 10. Wikis!
  11. 11. SEQwiki <ul><li>Describes tools for HTS analysis
  12. 12. using structured data for each tool
  13. 13. collected via forms to help enforce structure.
  14. 14. Provides data driven navigation. </li></ul>
  15. 23. DASWiki <ul><li>Model DAS data in the wiki.
  16. 24. Boils down to modelling GFF.
  17. 25. Can also model the whole registry... </li></ul>
  18. 28. <ul><li>DAS client configured to show a track from the DAS server.
  19. 29. Client queries the server for data.
  20. 30. Server uses the 'wiki adaptor' to query the wiki.
  21. 31. Wiki returns the queried data.
  22. 32. Data formatted as DAS.
  23. 33. Returned to the client. </li></ul>DAS Server Wiki adaptor Query API DAS Client DAS Wiki Query API
  24. 34. DAS Server Wiki adaptor Query API DAS Client DAS Wiki Query API
  25. 36. Justin's Wiki <ul><li>Wiki for plant genome annotation
  26. 37. A. thaliana + O. sativa GAF </li><ul><li>~10K annotations
  27. 38. ~50K wiki pages </li></ul></ul>
  28. 42. Git...
  29. 43. Git...
  30. 44. BioGit
  31. 45. The End
  32. 46. The End ?

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