Delivered Apr 2, 2013 at Redpath Museum auditorium, McGill University for Science and Museums, REDM400

1. Biodiversity Informatics
David P. Shorthouse, Université de Montréal

2. TrochosaterricolaThorell, 1856 Trochosaruricola(De Geer, 1778)

3. What is biodiversity informatics?
How are biodiversity data used?
How are biodiversity data made available?
What are the key challenges?
What are its organizations?
Where can I go for more?

4. Bioinformatics
focused on the *omics

5. Biodiversity Informatics
interoperability of scientific names,
classifications

6. History of “Biodiversity Informatics”
Canadian Biodiversity
Informatics Consortium (1993)
John S. Whiting

7. Johnson Norm F. 2007. Biodiversity
informatics. Annu Rev Entomol. 52:421-38.
DOI 10.1146/annurev.ento.52.110405.091259

8. Who, What,
Where, When?

10. http://www.simplemappr.net

11. How are biodiversity data used?

12. Chapman, A. D. 2005. Uses of Primary
Species-Occurrence Data, version 1.0.
Report for the Global Biodiversity
Information Facility, Copenhagen.

13. Uses of Primary Occurrence Data
1 Taxonomy: research, indices, floras/faunas, field guides,
phylogenies
2 Biogeography: distributional atlases, species distribution
modeling, species decline
3 Life Histories and Phenologies
4 Endangered, Migratory, and Invasive Species
5 Impact of Climate Change
6 Ecology, Evolution and Genetics: habitat loss, ecosystem
function
7 Environmental Planning: impact assessments
8 Conservation Planning: rapid biodiversity assessments,
identifying priority areas, reserve selection, sustainable use

14. Uses of Primary Occurrence Data
9 Health and Public Safety: disease and disease
vectors, bioterrorism, biosafety, parasitology
10 Bioprospecting
11 Border Control and Wildlife Trade
12 Education and Public Outreach
13 Ecotourism
14 Society and Politics: data repatriation
15 Recreational activities

16. DOI 10.7717/peerj.11

17. Dr. Jeremy Kerr, University of Ottawa

18. How are biodiversity data made
available?

19. The Process
Collect
Prepare
Digitize
Standardize
Publish

20. Collect
Why do we collect specimens?

21. Prepare
Creating a long-term voucher
for scientific research

23. Specimen label
Primary biodiversity data
What, when, where & who

24. What?
Scientific name & classification
• Anemone narcissiflora
• Anemone parviflora
• Anemone richardsonii
• Arabis lyrata
• Caltha leptosepala
• Campanula lasiocarpa
• Cardamine umbellata
• Carex aquatilis
• Carex capillaris
• Carex enanderi
• Carex gynocrates
• Carex podocarpa
• Carex vaginata
• Claytonia sarmentosa
• Corydalis pauciflora
• Dodecatheon frigidum
• Draba crassifolia
• Dryas integrifolia
• Epilobium anagallidifolium
• Epilobium latifolium
• Equisetum variegatum
• Eriophorum angustifolium
• Eriophorum brachyantherum

25. When?
Date -> trends

26. Where?
Locality, elevation & habitat

27. Georeferencing
Locality description -> Coordinates

28. Who?
Collector -> history

29. Locked in paper format
Not easily accessible

30. Digitize
Recording specimen information
in a digital format

31. Standardize
Different database systems
Different formats
Different languages

32. Darwin Core
A common biodiversity
information language
bit.ly/DarwinCore

33. 175 terms

34. Darwin Core Archive
A common biodiversity
information format

36. Simplify
Standardize Harvest
& publish
Tapir protocol GBIF’s
Database
central index
DarwinCore
Archive User

37. Publish
Make available online
GBIF Integrated Publishing Toolkit (IPT)

38. What are the key challenges?

39. DOI 10.1016/j.tree.2010.09.004

40. DOI 10.1007/11530084_8

41. Homonyms
same name for many taxa
Synonyms
different names for same taxa
Variant representations
orthography, spelling,
differences in authority

44. What are (a few of) the Biodiversity
Informatics organizations?

46. Global Names
Find Atomize Index
…{
genus: { epitheton: "Pardosa" },
species: {
basionymAuthorTeam: {
year: "1892”,
authorTeam: "Banks",
author: ["Banks”] },
epitheton: "moesta",
authorship: "Banks, 1892"
} http://gni.*
}…
http://gnrd.*
Resolve Edit
http://gnite.org
http://resolver.*
*.globalnames.org

47. Applying Global Names Tools
80
70
60
# Names found
50
40
30
20
t220 =, 3.68 p = 0.0003
10
0
Data Packages Published PDF

48. What about Canadian Organizations?
Federal Biodiversity Information Partnership
Canadian Biodiversity Information Facility
OBIS Canada

49. canadensys.net

50. A network
Of people and collections

51. Academic
11 universities, 5 botanical
gardens & 2 museums

52. Canadensys Headquarters
Université de Montréal
Biodiversity Centre

53. 35+ researchers
Mainly systematists

54. 30 collections
Plants, insects and fungi

55. 13 mil. specimens
2 out of 3 are insects

56. Goal
Mobilize 3 million specimen
records (20%) by 2013

59. Carole Sinou
Data Publication Support Professional

61. Download
Per dataset
Not very flexible

63. Checklists
Data about taxa (vs specimens)
Now also supported by
DwC-A, GBIF & IPT

64. VASCAN
Database of Vascular Plants of Canada
data.canadensys.net/vascan

67. Data license
Allow data to be used
bit.ly/cc0-for-data

68. Where can I go for more?

70. Biodiversity Informatics
Commercialization

71. What is biodiversity informatics?
How are biodiversity data used?
How are biodiversity data made available?
What are the key challenges?
What are its organizations?
Where can I go for more?

72. Thanks!
www.canadensys.net
@canadensys
@dpsSpiders
david.shorthouse@umontreal.ca
David P. Shorthouse