Biodiversity Informatics Course Presentation

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Roderic Page

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

Educación Tecnología

Ideas ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object]

Things we know …without knowing that we know

Melissotarsus insularis no hit CASENT0107663-D01 DQ176312 Melissotarsus sp. BLF m1 DQ176312 CASENT0107663-D01 Melissotarsus insularis 1 Melissotarsus insularis Melissotarsus sp. BLF m1 =

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

Visualising biodiversity digitisation in real time

Some of this knowledge is being broadcast using RSS

We want RSS feeds that ,[object Object],[object Object],[object Object]

like Geo RSS geotagged (latitude, longitude, woeid) taxonomic name (machine tags) timestamp

We can make it ourselves http://bioguid.info/rss Secret sauce (= screen scraping) Web page RSS

Then add tags using services Georeferencing Taxonomic names

Challenge: aggregate and display RSS Merge RSS feeds, add missing georeferencing and taxonomic names Display where, when, what

http://bioguid.info/ebio09/www/3d Visualising biodiversity digitisation in real time

Need tools to: ,[object Object],[object Object],[object Object]

The Carmen Electra argument for Open Access

Semantic wikis (or, what’s wrong with Wikipedia?)

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Biodiversity Informatics Course Presentation

1. Biodiversity Informatics

5. Linking

6. Apomys datae

9. Apomys specimen

10.

11. How do we integrate these data?

12. Why integrate?

13. Learn stuff we don’t know

14.

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.

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.

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?)

Notas del editor

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.

Biodiversity Informatics Course Presentation

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Notas del editor