Nice 2012, BioWikis and DASWiki

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Some slides showing some BioWikis developed using Semantic MediaWiki.

Some slides showing some BioWikis developed using Semantic MediaWiki.

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Transcript

  • 1. Some wikis I have known
  • 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. My world view...
  • 4. I WIKI
  • 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. Technology
    • MediaWiki
    • Semantic MediaWiki
  • 9. Wikis!
  • 10. Wikis!
  • 11. SEQwiki
    • Describes tools for HTS analysis
    • 12. using structured data for each tool
    • 13. collected via forms to help enforce structure.
    • 14. Provides data driven navigation.
  • 15.  
  • 16.  
  • 17.  
  • 18.  
  • 19.  
  • 20.  
  • 21.  
  • 22.  
  • 23. DASWiki
    • Model DAS data in the wiki.
    • 24. Boils down to modelling GFF.
    • 25. Can also model the whole registry...
  • 26.  
  • 27.  
  • 28.
    • DAS client configured to show a track from the DAS server.
    • 29. Client queries the server for data.
    • 30. Server uses the 'wiki adaptor' to query the wiki.
    • 31. Wiki returns the queried data.
    • 32. Data formatted as DAS.
    • 33. Returned to the client.
    DAS Server Wiki adaptor Query API DAS Client DAS Wiki Query API
  • 34. DAS Server Wiki adaptor Query API DAS Client DAS Wiki Query API
  • 35.  
  • 36. Justin's Wiki
    • Wiki for plant genome annotation
    • 37. A. thaliana + O. sativa GAF
      • ~10K annotations
      • 38. ~50K wiki pages
  • 39.  
  • 40.  
  • 41.  
  • 42. Git...
  • 43. Git...
  • 44. BioGit
  • 45. The End
  • 46. The End ?
  • 47.  
  • 48.  
  • 49.  
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  • 53.  
  • 54.