Talk given at CISA 2013, Barcelona, 26 September 2013

1. Biodiversity informatics: why
aren’t we there yet?
@rdmpage
http://iphylo.blogspot.com

2. I’ve often said I want a Google
for biodiversity data…

3. …turns out what I should have asked
for was a NSA for biodiversity

5. • 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

6. known
unknown
know
ns
unknowns

8. What do these diagrams tell us?

11. Implications
• Sequencing is cheap
• The flood of sequences is only going to increase
• How much of this is relevant to biodiversity?
• --

12. Numbers of new animal names
1923
WWI WWII

13. Implications
• Rate of new taxa being described is relatively
constant
• Suggests taxonomists are working at capacity
• Most taxonomic work is in the past
• Compare this to exponential growth of sequencing
• --

14. Mammals in GenBank
Proper Linnaean names
Aus sp.

15. Mammals
Proper Linnaean names
Aus sp.

16. “Invertebrates”
BOLD

17. Dark taxa
• Disconnect between taxonomy and genomics
• How much of this comprises taxa we already
know about versus new diversity?
• Do we need taxonomic names?
• --

18. 100,000 articles from http://biostor.org (BHL)
1923 today

19. Scanned legacy
• BHL is more than pre-1923 literature
• The real gap is post-1923 to pre-open access (2003)
• Most of the 20th
century taxonomic literature is
“dark”
• --

20. Size of Wikipedia articles on mammals
Few, large articles
Many, small
articles“long tail”

21. Power law
• We know a lot about a few species
• For most species we know very little (even in well-
known groups)
• For poorly known species need to go to legacy
literature
• --

22. PanTHERIA (2009)
1923 2003

23. Legacy literature
• Legacy literature matters (even for well-studied taxa)
• Much of this will be in digitally “dark” period
• --

24. Publishers of
taxonomy
(# articles)
http://bionames.org

25. Publishers
• BioStor (BHL) is the single largest source of
taxonomic literature
• Lots of tiny publishers (long tail)
• Commercial publishers important (Magnolia Press,
Springer, Informa, Wiley, Elsevier, BioOne)
• Who do we talk to about data mining?
• --

26. Taxonomic journals (articles/decade)

27. Implications
• Zootaxa is indeed a “mega journal”
• If we had to pick one journal to data mine it is
Zootaxa
• --

29. GBIF
• The Global Biodiversity Information Facility is not
evenly “global”
• Tells us as much about sampling as distribution of
diversity

30. Flickr EOL group

31. Crowd sourcing
• Where is the “crowd”?
• It’s where the iPhones are…

32. GenBank animal sequences

33. GenBank host records

34. Implications
• GenBank is about more than genes
• GenBank has a wealth of information on location,
and ecological interactions

36. Implications
• Phylogenetic data is not being archived (why not?)
• Makes it hard to reproduce studies
• Does data matter?
• What level of granularity should be citable?

37. What do these diagrams tell us?