Biodiversity Informatics Course Presentation

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Notes on slide 1

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.

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

+ rdmpagerdmpage, 2 months ago

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