Going Digital

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Invited talk given at The Natural History Museum, London, 17 March 2009 (I gave a very similar talk at the Department of Zoology, University of Stockholm, 12 March 2009).

Invited talk given at The Natural History Museum, London, 17 March 2009 (I gave a very similar talk at the Department of Zoology, University of Stockholm, 12 March 2009).

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  • All this can be applied to museums (and libraries and archives) across the board and not just to natural history collections
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  • 1. Going Digital Rod Page Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
  • 2. If you are not online you are invisible (Web 1.0)
  • 3. All useful information will be online (Web 1.0)
  • 4. Value is explicit and based on usage (links) (Web 1.0)
  • 5. Reputation is created… (Web 2.0)
  • 6. …not conferred by authority (Web 2.0)
  • 7. Everything will have a URL (Web 3.0)
  • 8. Yes, I’ve drunk the Kool Aid
  • 9. …but I’m not alone
  • 10. Social networking
  • 11. Dinosaurs ban it
  • 12. Scaremongers say it causes cancer
  • 13. Some “get it”
  • 14. Some do real work with it
  • 15. #uksnow
  • 16. @kzelnioCould you do me a favour: 10.1016/j.anbehav.2008.12.017
  • 17. Where is the (digital) museum? Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
  • 18. www.nhm.ac.uk
  • 19. Zoology
  • 20. This dataset is not accessible by the public. For more information please contact the Department of Zoology.
  • 21. Silo http://www.flickr.com/photos/kenmccown/132990634/
  • 22. 404
  • 23. GBIF http://www.flickr.com/photos/chrisfreeland/3306689322/
  • 24. Top 10 GBIF data providers
  • 25. League table Museum GBIF data Open access Staff Social journal publications Networking online Twitter, yes 3,446,016 Facebook, Youtube, etc. (searchable yes collections) (Twitter) 412,797 (planned) (planned)
  • 26. Why go digital? Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
  • 27. Diverse kinds of data
  • 28. Apomys datae
  • 29. Apomys specimen
  • 30. How do we integrate these data?
  • 31. Why integrate?
  • 32. Learn stuff we don’t know
  • 33. • There are knownknowns, things we know that we know • There are knownunknowns, things we now know we don’t know • But there are also unknownunknowns, things we do not know we don't know
  • 34. Unknown knowns
  • 35. Things we know …without knowing that we know
  • 36. Melissotarsus insularis
  • 37. 1 Melissotarsus insularis no hit Melissotarsus insularis CASENT0107663-D01 CASENT0107663-D01 DQ176312 DQ176312 Melissotarsus sp. BLF m1 = Melissotarsus sp. BLF m1 Melissotarsus insularis
  • 38. No one source has all the answers
  • 39. Joining the dots
  • 40. Identifiers
  • 41. Digital Object Identifier (DOI)
  • 42. Identifies a publication
  • 43. Globally unique
  • 44. 10.1016/j.ympev.2006.04.006
  • 45. Paper
  • 46. Why have DOIs?
  • 47. Link rot
  • 48. Refs
  • 49. Cites 2006 2006
  • 50. Forward Cites 2006 2009
  • 51. Shoulders of giants
  • 52. progress is incremental
  • 53. reuse past results
  • 54. Forward Cites 2006 2008
  • 55. Species Genes
  • 56. data linking
  • 57. data citation
  • 58. http://iphylo.org/~rpage/challenge
  • 59. demo
  • 60. Vision
  • 61. Chromiscircumaurea
  • 62. What should museums do? Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
  • 63. Do nothing Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
  • 64. The new
  • 65. Don’t try this at home • Image storage (Flickr) • Video storage (YouTube, Vimeo) • Bibliographies (Connotea, Mendeley) • Social networking (Facebook, Twitter) • Annotation (CMS, Wikis, Blogs) • Bulk storage (Amazon S3) • Bulk computing (Amazon EC2)
  • 66. Make it easy Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
  • 67. http://www.flickr.com/photos/scobleizer/2256358640/
  • 68. http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
  • 69. http://abacus.gene.ucl.ac.uk/software/paml.html
  • 70. http://mrbayes.csit.fsu.edu/
  • 71. http://www.tree-puzzle.de/
  • 72. http://atgc.lirmm.fr/phyml/
  • 73. No branding
  • 74. No corporate style
  • 75. No permission needed
  • 76. Institution provides infrastructure…
  • 77. …then gets out of the way
  • 78. Top five European papers in evolutionary biology 1996-2006 1,118 – 4,512 citations
  • 79. Partnerships (EOL) Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
  • 80. “Dance of the initiatives” Christine Hine
  • 81. Danger of too much money
  • 82. Million Dollar Page
  • 83. EOL in it’s present form
  • 84. sucks
  • 85. Can I do science with it?
  • 86. Not yet…
  • 87. Intellectual Property Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
  • 88. Fear
  • 89. Ignorance
  • 90. Silo http://www.flickr.com/photos/kenmccown/132990634/
  • 91. AMNH Conditions 1. Except as otherwise expressly stated herein, the information, records, or images in these databases may not be reproduced, distributed, or publicly displayed, in whole or in part, without the express written permission of the American Museum of Natural History (AMNH). 2. AMNH does not grant permission for anyone to use, download, reproduce, publicly display, distribute, or reprint all or substantially all of the information, records, or images in the database. 3. Subsets of the information, records, or images in the database may be used, downloaded, reproduced, publicly displayed, distributed, or reprinted strictly for educational, scientific, scholarly, and other non-profit uses provided that AMNH is appropriately cited as the source of the information. 4. Subsets of the records from the database downloaded for use with data from other data sets must be clearly identified by the attribution “AMNH.” 5. Data are provided to individual users with the understanding that said data will not be passed on to third parties or redistributed, except with approval from AMNH. 6. …
  • 92. 2. AMNH does not grant permission for anyone to use, download, reproduce, publicly display, distribute, or reprint all or substantially all of the information, records, or images in the database.
  • 93. Elachistocleisovalis http://www.flickr.com/photos/lleonebio/3328398741/
  • 94. You know more than the AMNH database does!
  • 95. DQ283405 FEATURES Location/Qualifiers source 1..2400 /organism=quot;Elachistocleisovalisquot; /organelle=quot;mitochondrionquot; /mol_type=quot;genomic DNAquot; /specimen_voucher=quot;AMNH A141136quot; /db_xref=quot;taxon:367647quot; /country=quot;Guyana: Dubulay Ranch on the Berbice River, 200ft, 5'40'55N, 57'51'32Wquot; misc_RNA<1..>2400 /note=quot;contains 12S ribosomal RNA, tRNA-Val, and 16S ribosomal RNAquot;
  • 96. Tens of thousands of copies all around the world
  • 97. AMNH Conditions 1. Except as otherwise expressly stated herein, the information, records, or images in these databases may not be reproduced, distributed, or publicly displayed, in whole or in part, without the express written permission of the American Museum of Natural History (AMNH). 2. AMNH does not grant permission for anyone to use, download, reproduce, publicly display, distribute, or reprint all or substantially all of the information, records, or images in the database. 3. Subsets of the information, records, or images in the database may be used, downloaded, reproduced, publicly displayed, distributed, or reprinted strictly for educational, scientific, scholarly, and other non-profit uses provided that AMNH is appropriately cited as the source of the information. 4. Subsets of the records from the database downloaded for use with data from other data sets must be clearly identified by the attribution “AMNH.” 5. Data are provided to individual users with the understanding that said data will not be passed on to third parties or redistributed, except with approval from AMNH. 6. …
  • 98. You are going digital whether you like it or not…
  • 99. If it is on the web it will be found, and used
  • 100. This is a good thing
  • 101. Creative Commons
  • 102. Why be open? Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
  • 103. Caeciliidae
  • 104. Caeciliidae
  • 105. Caeciliidae
  • 106. Pagelluserythrinus
  • 107. Pagelluserythrinus
  • 108. Pagelluserythrinus
  • 109. Mannophrynetrinitatis MVZ 199838 MVZ 199828 (Aneidesflavipunctatus)
  • 110. Errors in databases
  • 111. Errors in publications
  • 112. The Carmen Electra argument for Open Access
  • 113. treemap
  • 114. reuse data
  • 115. Electra pilosa
  • 116. Carmen Electra versus Electra (guess who wins…)
  • 117. reuse data
  • 118. Homo sapiens
  • 119. AJ711044
  • 120. should be AJ971044
  • 121. How do we find and fix these errors?
  • 122. Don’t release data until it is “perfect” (wrong)
  • 123. “given enough eyes, all bugs are shallow” Eric S Raymond
  • 124. Credit Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
  • 125. Google Page Rank 1.49 A 0.78 B C 1.58 0.15 D
  • 126. Page rank for web page
  • 127. Scientific citation
  • 128. H-index for authors
  • 129. Impact factor for journals
  • 130. What about an impact factor for data?
  • 131. Metric of the value of the data
  • 132. Incentive to have globally unique, citable identifiers
  • 133. What to digitise first? Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/
  • 134. First digitise that which has been cited
  • 135. W D Lang Nature 139, 191 (1937) doi:10.1038/139191a0
  • 136. http://www.flickr.com/photos/mtl_shag/1403957285/
  • 137. www.nhm.ac.uk
  • 138. V S Smith
  • 139. …end Photo by Keith Marshall http://www.flickr.com/photos/keithmarshall/432924465/