Biodiversity informatics involves making biodiversity data accessible through digitization, standardization, and publishing. Biodiversity data is used for taxonomy, biogeography, endangered species monitoring, and more. Key challenges include resolving scientific names and data quality. Major organizations include GBIF, Global Names, and Canadensys which works to mobilize Canadian specimen records. Additional resources can be found through conferences, organizations, and online communities.

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

2. © Mr.checker (CC-SA 3.0 Unported)

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”
John S. Whiting
Canadian Biodiversity
Informatics Consortium (1993)

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

9. Who, What,
Where, When?

10. How are biodiversity data used?

11. Chapman, A. D. 2005. Uses of Primary
Species-Occurrence Data, version 1.0.
Report for the Global Biodiversity
Information Facility, Copenhagen.
http://www.gbif.org/resources/2834

12. 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
Uses of Primary Occurrence Data

13. Uses of Primary Occurrence Data
8 Conservation Planning: rapid biodiversity
assessments, identifying priority areas, reserve
selection, sustainable use
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

15. DOI 10.7717/peerj.11

16. DOI 10.1038/nature12872

17. How are biodiversity data made
available?

18. The Process
Collect
Prepare
Digitize
Standardize
Publish

19. Collect
© Ainsley Seago

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

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

23. Digitize
Recording specimen information
in a digital format

24. Standardize
Different database systems
Different formats
Different languages

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

26. 175 terms

27. Darwin Core Archive
A common biodiversity
information format

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

30. What Other Kinds of Data?
Images
Observations
Phylogenetic Trees
Graphs
Unstructured texts
Taxonomic lists

31. What are the key challenges?

32. Scientific Names

33. DOI 10.1007/11530084_8

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

36. DOI 10.1016/j.tree.2010.09.004

37. Globally Unique Identifiers

38. Data Quality and Fitness-for-Use

39. Giving Credit for Participation &
Metrics of Success

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

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

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

44. canadensys.net

45. Academic
11 universities, 5 botanical
gardens & 2 museums
35+ researchers

46. 30 collections
Plants, insects and fungi

47. Canadensys Headquarters
Université de Montréal
Biodiversity Centre

48. 13 mil. specimens
2 out of 3 are insects

49. Goal
Mobilize 3 million specimen
records (20%)

52. Download
Per dataset
Not very flexible

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

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

57. Biological Survey of Canada
The Biota of Canada
http://www.biologicalsurvey.ca

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

59. Where can I go for more?

60. Social Venues
TAXACOM
TDWG
Canadensys Google Group
iDigBio
ECN-L
GitHub
Twitter

61. What Skills/Technologies
Might I Need?
Web programming: HTML5, css
Relational databases: PostgreSQL/PostGIS,
MySQL
NoSQL data stores: Neo4j, CouchDB
Programming languages: R, Python, ruby, Java,
JavaScript
Creativity with data: dynamic visualizations

62. Biodiversity Informatics
Commercialization
iekho.com
Branché

63. 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?

64. www.canadensys.net
@canadensys
@dpsSpiders
david.shorthouse@umontreal.ca
David P. Shorthouse