Talk ontaxonomy, identifiers, and links given at pro-iBiosphere meeting, Leiden, 13 February 2013

1. @rdmpage
http://iphylo.blogspot.com
Why the semantic web is more than PDF
The semantic web and taxonomy
Surfacing the deep data of taxonomy
Something about links

2. @mycokeys
10.3897/mycokeys.5.4302

4. Where are:
• The users?
• The questions?
• The science?

7. Phylogeography

8. Taxonomy

9. Our questions span multiple
databases
(“paths” in network)

10. Specimens and diseases

11. PMID:948206

12. http://biostor.org/reference/102054

14. http://data.gbif.org/occurrences/215921922/

16. BHL and GBIF as biomedical databases
http://iphylo.blogspot.co.uk/2012/03/bhl-and-gbif-as-biomedical-databases.html

17. Metrics

18. In an attempt to live up to that increasing
demand for documentation, the leadership of
the Natural History Museum of Denmark has
issued an order to its curatorial staff - The
staff members are requested to document
which publications from 2011, written
entirely by external scientists, that in one way
or another are based on material in the
collections of the Museum.
@TAXACOM http://markmail.org/message/opv2we7fkmro2nen

19. https://twitter.com/#!/search/10.1371%252Fjournal.pone.0036881

20. https://twitter.com/edwbaker/status
/205595933159858176
https://twitter.com/edwbaker/status/205595933159858176

21. http://www.museum-analytics.org/

22. Impact of
collection

23. Cited, linkable specimens
NMNH Vertebrate Zoology
11194
Herpetology Collections
Herpetology Collection (University
of Kansas Biodiversity Research 9619
Center)
CAS Herpetology Collection Catalog 6720
MCZ Herpetology Collection 5818
http://iphylo.blogspot.co.uk/2012/02/gbif-specimens-in-biostor-who-are-top.html

24. The story of the web
(it’s all about links)

25. http://… http://…

26. http://… http://…
link
,

27. http://… http://…
http://…

28. http://… http://…
person book
is a author of
Fred
http://…

29. The Semantic web:
“The future of the web
…and always will be”
– Peter Norvig (Google)

30. http://… http://…
person book
is a author of
Fred
http://…

31. http://… http://…
http://…

32. Without links we will #fail to
deliver the cool stuff

33. http://… http://…
link
,

34. Links = pairs of identifiers

35. Problem:
nobody sees value in the links

36. @mycokeys
10.3897/mycokeys.5.4302

37. Publishers
Museums
Genomics

38. Question 1:
When will we value links enough
to create and maintain them?

39. #@$! GBIF keeps changing URLs!
http://iphylo.blogspot.co.uk/2012/07/dear-gbif-please-stop-changing.html

40. Citation network = valuable links

41. Question 2:
How do we link in the absence of
identifiers?

42. When shall we link?
http://go-to-hellman.blogspot.co.uk/2010/04/when-shall-we-link.html

43. When shall we link?
• Just in case (hard coded)
– Identifiers
– e.g., DOIs
• Just in time (link when needed)
– Instructions to make link
– OpenURL

44. Just in case
doi:10.1186/1471-2105-12-187
Just in time
?journal=BMC Bioinformatics
&volume=12&spage=187

45. The challenge:
How do we make persistent links
in the absence of persistent
identifiers?