The document discusses how taxonomy data is increasingly available in digital formats, with names, publications, and sequences stored in databases. However, the majority of taxonomic names are still only found in the legacy scientific literature not available online. Creating a single comprehensive database of all scientific names linked to their original publications and other related data would help resolve issues around ambiguous names and dark taxa. However, this remains a significant challenge due to the vast amount of legacy literature not currently accessible or digitized.

1. Surfacing the deep data of taxonomy
@rdmpage
http://iphylo.blogspot.com

2. To a first approximation the
taxonomy of life is already digital…

3. doi:10.1126/science.276.5313.734

4. Data – GenBank
Publications – PubMed
Names – Names4Life

5. So, we’re done! (aren’t we?)

6. doi:10.1126/science.276.5313.734

8. Zoology as microbiology
Microbiology Zoology
GenBank ➔ DNA barcoding
PubMed ➔ Digital archives (BHL)
Names ➔ ION, ZooBank, uBio, …
Images from http://phylopic.org

9. Why does having a single
database of names matter?

10. Bacterial names linked to literature
http://dx.doi.org/10.1099/ijs.0.035154-0

11. Paenibacillus polymyxa
• http://dx.doi.org/10.1601/nm.5110 (name)
• http://dx.doi.org/10.1601/tx.5110 (taxon)
​
Image from http://dx.doi.org/10.1128/AEM.71.11.7292-7300.2005

12. …still not convinced?

14. Skull, mandible and tooth morphology of the holotype of L. melvillei MUSM 1676.
O Lambert et al. Nature 466, 105-108 (2010) doi:10.1038/nature09067

15. Leviathan melvillei

17. Bugger…

18. Livyatan melvillei

19. Two kinds of #fail

20. We don’t have a list of all names

21. Publications containing names
often not accessible

22. Leviathan melvillei

23. Need more convincing?

24. Dark taxa
http://iphylo.blogspot.co.uk/2011/04/dark-taxa-genbank-in-post-taxonomic.html

25. Mammals in GenBank
Aus sp.
Proper Linnaean names

26. Mammals
Aus sp.
Proper Linnaean names

27. “Invertebrates”
BOLD

28. Is this a problem?

29. It’s the norm for Bacteria

30. Dark taxa will only increase in
number

31. Roth v. Wikipeia
http://www.newyorker.com/online/blogs/books/2012/09/an-open-letter-to-wikipedia.html

32. Wikipedia says “no”

33. “I understand your point that the
author is the greatest authority on
their own work,” writes the Wikipedia
Administrator—“but we require
secondary sources.”

34. @quominus
One of Wikipedia’s core principles, along
with things like neutrality, is verifiability:
a reader must be able to look at a
statement in a Wikipedia article and find
out where it comes from.
http://quominus.org/archives/981

35. Taxonomic statements should be
verifiable

36. Literature is the
evidence base for taxonomy

37. Literature online
Commercial
publishers
Digital archives
Museums,
universities,
and scientific
societies

38. http://iphylo.org/~rpage/itaxon

39. Animal names per decade
Data from http://www.organismnames.com

40. Names with a DOI
25%

41. BioStor (BHL)
25%
©
@biostor_org
http://biostor.org

42. Online
(DOI, BioStor, JSTOR,DSpace,PDF, …)
50%

43. Identifiers

44. Vast majority of names are in the
legacy literature

45. Zootaxa and Zookeys
XML

46. My wish list…

47. Names linked to:
literature
specimens
geography
sequences
phylogeny…

49. BioNames
(real soon now…)
Computable Data Challenge