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Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
Biodiversity Informatics Course Presentation
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Biodiversity Informatics Course Presentation

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Slides from a presentation to Biodiversity Informatics course, Stockholm, 16-09-2009

Slides from a presentation to Biodiversity Informatics course, Stockholm, 16-09-2009

Published in: Education, Technology
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  • This is a great overview with real world examples that we're wrangling with now. Great to see your work towards solving many of these issues too. Also, +1 for the Rumsfeld quote, it's worth repeating...
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  • ok, will pay 'cool'.
    was using quote compilation sites like:
    http://www.brainyquote.com/quotes/authors/n/nicolaus_copernicus_2.html
    http://thinkexist.com/quotation/to_know_that_we_know_what_we_know-and_to_know/201808.html
    etc.
    Real Media? you are kidding me! #bbc #fail
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  • Yeah but Rumsfeld is cooler. Plus we know he said this (http://news.bbc.co.uk/media/audio/38078000/rm/_38078601_rummer.ram), whereas Googling suggests it's not clear who said 'To know that we know what we know, and to know that we do not know what we do not know, that is true knowledge'.
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  • slide 14 - you might like to contrast the oft-quoted ramblings of Rumsfeld with the more erudite, succinct and poetic 'To know that we know what we know, and to know that we do not know what we do not know, that is true knowledge'
    of Copernicus.
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  • This ant illustrates a case where three different data source (NCBI, AntWeb, journal supplementary material) are needed to discover that, in fact, GenBank has sequences for this ant.
  • If you search NCBI for “Melissotarsus insularis” you find nothing. If you search AntWeb you find some specimens, one of which is CASENT0107663-D01. In the Phils Trans barcoding paper the supplementary material (also online in BoLD) shows that CASENT0107663-D01 has been sequenced, yielding a COI sequence with accession number DQ176312. If you go back to GenBank and look up the accession number you discover the taxon “ Melissotarsus sp. BLF m1”, which must be the same as Melissotarsus insularis. Hence, GenBank should actually say “yes, I have information on Melissotarsus insularis”. There is latent knowledge in these data sources that we miss if they remain in ignorance of each other.
  • http://www.wired.com/images/article/magazine/1610/ff_barcodeoflife4_f.jpg
  • Leptotyphlops carlae
  • http://species.asu.edu/2009_species04
  • ~/Desktop/GrandChallenge/Data/DVD/LAB0370A/10557903/00420003/06003691/main.xml
  • Citation, user sees bibliography and may be able to follow links
  • Data citation with PageRank scores
  • http://www.flickr.com/photos/bastique/639784702/ by bastique
  • History flow visualisation, after Jeff Atwood’s animated GIF
  • Afrotheria
  • EOL is like Wikipedia, but not. This difference may prove it’s downfall.
  • For the species in Wikipedia I asked what web site comes top of the Google search for that name. Wikipedia dominates the search ranking. There really is only one game in town.
  • Transcript

    • 1. Biodiversity Informatics
    • 2.  
    • 3.  
    • 4. Ideas
      • Linking
      • Mashups
      • Data mining
      • RSS
      • Identifiers
      • Errors
      • Wikis
    • 5. Linking
    • 6. Apomys datae
    • 7.  
    • 8.  
    • 9. Apomys specimen
    • 10.  
    • 11. How do we integrate these data?
    • 12. Why integrate?
    • 13. Learn stuff we don’t know
    • 14.
      • There are known knowns , things we know that we know
      • There are known unknowns , things we now know we don’t know
      • But there are also unknown unknowns , things we do not know we don't know
    • 15. Unknown knowns
    • 16. Things we know …without knowing that we know
    • 17. Melissotarsus insularis
    • 18. Melissotarsus insularis no hit CASENT0107663-D01 DQ176312 Melissotarsus sp. BLF m1 DQ176312 CASENT0107663-D01 Melissotarsus insularis 1 Melissotarsus insularis Melissotarsus sp. BLF m1 =
    • 19. No one source has all the answers
    • 20. Joining the dots
    • 21. Mashups
    • 22.  
    • 23. Single source
    • 24. Many sources
    • 25.  
    • 26. Combine sources
    • 27.  
    • 28. ispecies.org
    • 29.  
    • 30.  
    • 31. Merge things your way
    • 32. Don’t like iSpecies?
    • 33. Make your own!
    • 34.  
    • 35.  
    • 36. Data mining
    • 37.  
    • 38. Text mining
    • 39. Morphological and molecular description of Haematoloechus meridionalis n. sp. (Digenea: Plagiorchioidea: Haematoloechidae) from Rana vaillanti brocchi of Guanacaste, Costa Rica Halipegus eschi n. sp. (Digenea: Hemiuridae) in Rana vaillanti from Guanacaste Province, Costa Rica Haematoloechus danbrooksi n. sp. (Digenea: Plagiorchioidea) from Rana vaillanti from Los Tuxtlas, Veracruz, Mexico
    • 40. RSS
    • 41.  
    • 42. Visualising biodiversity digitisation in real time
    • 43. gathering new data…
    • 44. discovering new species…
    • 45. publishing papers…
    • 46. Some of this knowledge is being broadcast using RSS
    • 47. We want RSS feeds that
      • Have timestamps
      • Are georeferenced
      • Have taxonomic names as tags
    • 48. like Geo RSS geotagged (latitude, longitude, woeid) taxonomic name (machine tags) timestamp
    • 49. But what if no RSS?
    • 50. We can make it ourselves http://bioguid.info/rss Secret sauce (= screen scraping) Web page RSS
    • 51. Then add tags using services Georeferencing Taxonomic names
    • 52. Now we have RSS…
    • 53.
    • 54. … is anybody listening?
    • 55. Challenge: aggregate and display RSS Merge RSS feeds, add missing georeferencing and taxonomic names Display where, when, what
    • 56. http://bioguid.info/ebio09/www/3d Visualising biodiversity digitisation in real time
    • 57. Identifiers
    • 58. Digital Object Identifier (DOI)
    • 59.  
    • 60. Identifies a publication
    • 61. Globally unique
    • 62. 10.1016/j.ympev.2006.04.006
    • 63. Paper
    • 64. Why have DOIs?
    • 65. Link rot
    • 66. Refs
    • 67.  
    • 68.  
    • 69. Cites 2006 2006
    • 70. Forward Cites 2006 2009
    • 71. Shoulders of giants
    • 72. progress is incremental
    • 73. reuse past results
    • 74. Forward Cites 2006 2008
    • 75.  
    • 76. Species Genes
    • 77. data linking
    • 78. data citation
    • 79.  
    • 80. Need tools to:
      • Resolve identifiers
      • Create new identifiers
      • Find existing identifiers
    • 81. http://bioguid.info/openurl/
    • 82. Errors
    • 83. http://iphylo.org/~rpage/challenge
    • 84. demo
    • 85. The Carmen Electra argument for Open Access
    • 86. reuse data
    • 87. Electra pilosa
    • 88. Carmen Electra versus Electra
    • 89. reuse data
    • 90. Homo sapiens
    • 91. AJ711044
    • 92. should be AJ971044
    • 93. how do I fix this error?
    • 94. Closed
    • 95. Can’t easily fix
    • 96. Open…
    • 97. … and editable
    • 98. Anybody could fix it
    • 99. Wikis
    • 100. Wikis
    • 101. Versions 1 2 3 4 History flow
    • 102. Afrotheria
    • 103. EOL
    • 104.  
    • 105. Semantic wikis (or, what’s wrong with Wikipedia?)

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