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The Sam Adams talk

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Invited talk given at the National Museum of Natural History, Smithsonian Institution, 22 September 2016

Published in: Science
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The Sam Adams talk

  1. 1. The Sam Adams talk @rdmpage http://iphylo.blogspot.com
  2. 2. Numbers of new animal names 1923 WWI WWII
  3. 3. Implications • Taxonomists are working at capacity • Maybe we are running out of species to discover…(!) • Most taxonomic work is in the past (“legacy”)
  4. 4. Two graphs
  5. 5. Two graphs taxonomy
  6. 6. Focus on sequences = focus on phylogeny taxonomy
  7. 7. OneZoom.org
  8. 8. Visualise all barcodes http://iphylo.org/~rpage/bold-map
  9. 9. Page R. Visualising Geophylogenies in Web Maps Using GeoJSON. PLOS Currents Tree of Life. 2015 Jun 23 . Edition 1. doi: 10.1371/currents.tol.8f3c6526c49b136b98ec28e00b570a1e
  10. 10. Setting taxonomic information free taxonomy
  11. 11. Digitise the literature http://biodiversitylibrary.orghttp://biostor.org
  12. 12. BioNames http://bionames.org • 5 million (animal) names • 1.6 million with publications • 454,000 publications with digital identifier • DOIs, BHL, BioStor, PDFs, Gallica, etc.
  13. 13. Rethinking publications
  14. 14. Ted Nelson Hyperlinks and hypermedia Two-way links and “transclusion” = Xanadu Tim Berners-Lee HTTP, URL, HTML One-way links = world wide web
  15. 15. Web page Other web page Web linking, one way, document-level, “target” doesn’t know that it is linked to (“cited”), link can break (404)
  16. 16. text Work Source text Xanadu linking, two way, fragment-level, “source” knows it is linked to, source content is embedded, links don’t break
  17. 17. Xanadu
  18. 18. Wait, WTF has this to do with floras?!
  19. 19. A New Account of the Genus Horsfieldia (Myristicaceae), Pt 2 W J J O De Wilde The Gardens' bulletin, Singapore 38(1): 55-144 (1985) http://biostor.org/reference/175018 Horsfieldia lancifolia
  20. 20. Flora Malesiana. Series I - Seed Plants, Volume 14. Myristicaceae
  21. 21. Description Description Flora Article
  22. 22. van Balgooy 3973 van Balgooy 3973
  23. 23. Description Article Specimen { "key": 1139234988, "scientificName": "Horsfieldia lancifolia W.J.J.O. de Wilde", "kingdom": "Plantae", "phylum": "Tracheophyta", "order": "Magnoliales", "family": "Myristicaceae", "genus": "Horsfieldia", "species": "Horsfieldia lancifolia", "genericName": "Horsfieldia", "specificEpithet": "lancifolia", "taxonRank": "SPECIES", "decimalLongitude": 121.75, "decimalLatitude": -2.25, "continent": "ASIA", "stateProvince": "Sulawesi", "year": 1979, "month": 7, "day": 11, "occurrenceID": "http://data.biodiversitydata.nl/naturalis/spe cimen/L.1769594” } Data (GBIF) Data
  24. 24. Xanadu in the 21st century?
  25. 25. text Article Annotations table annotation annotation
  26. 26. @hypothes_is
  27. 27. Annotating a scientific paper
  28. 28. Aggregating annotations (iPhylo) http://iphylo.blogspot.co.uk/2016/06/aggregating-annotations-on-scientific_30.html
  29. 29. Towards a biodiversity knowledge graph Research Ideas and Outcomes 2: e8767 (07 Apr 2016) doi: 10.3897/rio.2.e8767
  30. 30. GBIF and the problem of data
  31. 31. Data and feedback flow Something’s wrong!
  32. 32. GBIF and the zika virus http://iphylo.blogspot.co.uk/2016/04/the-zika-virus-gbif-and-missing.html
  33. 33. What if we treat data like source code Original data Edited data
  34. 34. Summary • Sequencing versus taxonomy? • Visualisation as a tool • Rethinking the nature of publications • The Biodiversity Knowledge Graph • Data as source code

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