What do accessible occurrence data and checklists tell us about species diversity in Canada?

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This document discusses accessible occurrence data and checklists in Canada and what they can tell us about species diversity. It notes that over 11 million occurrence records are available on GBIF from Canada. While these data are accessible, many records have outdated taxonomy or lack location coordinates. The document encourages making checklist data openly available but notes it requires curation. Opportunities for innovative research using these biodiversity data are mentioned.

Science

What do accessible occurrence
data and checklists tell us about
species diversity in Canada?
David P. Shorthouse
Université de Montréal / Canadensys
@dpsSpiders

Discoverable
Computable
Standards
Digital
Open

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

Open
• Legally unrestrictive
• Openly licensed
• Can be reused, reconstituted, recombined
republished
FINE PRINT
The Canadian Museum of Nature owns the copyright
of almost all information (data and images) accessed
through its databases.
Data may not be transferred to another database for
distribution to others without prior written permission
from the Canadian Museum of Nature.

The Goal
• Establish provenance
• Track citations & metrics of use
• Build new networks of collaboration
• Play a significant role in « Big Data »

Innovation happens when you use
someone else’s data

Are Occurrence and
Checklist Data in Canada
Accessible?

Carabidae on Canadensys
Bembidion (Bracteon) punctatostriatum
Credit: Henri Goulet

Species at Risk on Canadensys
24 specimens
Cypripedium candidum Muhl. ex Willd.
Small White Lady’s-slipper
ENDANGERED
5 specimens
Antennaria flagellaris (A. Gray) A. Gray
Stoloniferous Pussytoes
ENDANGERED

doi: 10.3897/zookeys.283.4674
doi: 10.5886/txsd3at3

How do we deliver high
quality products?

Utility of « Accessible » Occurrence Data
Hjarding, A., Tolley, K. A., & Burgess, N. D. 2014. Red List assessments of East
African chameleons: a case study of why we need experts. Oryx
DOI 10.1017/s0030605313001427
Photographer: H. Vannoy Davis
« 99.9%of GBIF records
used outdated taxonomy
and 20% had no locality
coordinates »

What Can We Mine Now?
http://canent.shorthouse.net
https://github.com/dshorthouse/article_semanticizer

Upcoming Events
Canadensys new research initiatives workshop
Anne Bruneau, anne.bruneau@umontreal.ca
http://www.canadensys.net/2014/workshop-proposal
Data Publication Workshop K.W. Neatby Building:
January 13, 14, 2015; co-located in Tallahassee, FL with
iDigBio
James Macklin, james.macklin@agr.gc.ca
David Shorthouse, david.shorthouse@umontreal.ca

Take Home
• « Accessible » means computable & open
• Occurrence and checklist data can be
published, but they require curation
– Seek assistance from Canadensys & elsewhere
• There are significant challenges, but we can be
creative
• What new, innovative research can we do with
these data?

What do accessible
occurrence data and checklists
say about us?
@dpsSpiders

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What do accessible occurrence data and checklists tell us about species diversity in Canada?

1. What do accessible occurrence data and checklists tell us about species diversity in Canada? David P. Shorthouse Université de Montréal / Canadensys @dpsSpiders

2. Accessible

3. Discoverable Computable Standards Digital Open

4. Discoverable

5. DOI 10.1007/11530084_8

6. Computable

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

8. Digital

9. Open • Legally unrestrictive • Openly licensed • Can be reused, reconstituted, recombined republished FINE PRINT The Canadian Museum of Nature owns the copyright of almost all information (data and images) accessed through its databases. Data may not be transferred to another database for distribution to others without prior written permission from the Canadian Museum of Nature.

10. The Goal • Establish provenance • Track citations & metrics of use • Build new networks of collaboration • Play a significant role in « Big Data »

11. Innovation happens when you use someone else’s data

12. Are Occurrence and Checklist Data in Canada Accessible?

13. http://www.gbif.org/country/CA 11M!

14.

15.

16. Carabidae on Canadensys Bembidion (Bracteon) punctatostriatum Credit: Henri Goulet

17. Species at Risk on Canadensys 24 specimens Cypripedium candidum Muhl. ex Willd. Small White Lady’s-slipper ENDANGERED 5 specimens Antennaria flagellaris (A. Gray) A. Gray Stoloniferous Pussytoes ENDANGERED

18. doi: 10.3897/zookeys.283.4674 doi: 10.5886/txsd3at3

19. What Checklist Data Are Accessible?

20.

21. Challenges

22. How do we deliver high quality products?

23. Utility of « Accessible » Occurrence Data Hjarding, A., Tolley, K. A., & Burgess, N. D. 2014. Red List assessments of East African chameleons: a case study of why we need experts. Oryx DOI 10.1017/s0030605313001427 Photographer: H. Vannoy Davis « 99.9%of GBIF records used outdated taxonomy and 20% had no locality coordinates »

24. How do we reduce the workload?

25. http://miningbiodiversity.org

26. What Can We Mine Now? http://canent.shorthouse.net https://github.com/dshorthouse/article_semanticizer

27. Upcoming Events Canadensys new research initiatives workshop Anne Bruneau, anne.bruneau@umontreal.ca http://www.canadensys.net/2014/workshop-proposal Data Publication Workshop K.W. Neatby Building: January 13, 14, 2015; co-located in Tallahassee, FL with iDigBio James Macklin, james.macklin@agr.gc.ca David Shorthouse, david.shorthouse@umontreal.ca

28. Take Home • « Accessible » means computable & open • Occurrence and checklist data can be published, but they require curation – Seek assistance from Canadensys & elsewhere • There are significant challenges, but we can be creative • What new, innovative research can we do with these data?

29. What do accessible occurrence data and checklists say about us? @dpsSpiders

Editor's Notes

Loaded term What does this mean? « Able to be reached or entered »
Homonyms same name for many taxa Synonyms different names for same taxa Variant representations orthography, spelling, differences in authority Requires infrastructure or the capacity to reconcile scientific names and their surrogates (eg taxon concepts)
TODO: - Data for red-listed species in Canada (SARA)
The project is an international collaboration between the National Centre for Text Mining (UK), Missouri Botanical Garden (US), Dalhousie University’s Big Data Analytics Institute (Canada) and Ryerson University’s Social Media Lab (Canada). NaCTeM was also a recipient of the 2011 Digging into Data call with the Integrated Social History Environment for Research (ISHER) project. Started March 2014

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