Biodiversity Informatics
David P. Shorthouse, Université de Montréal
© Mr.checker (CC-SA 3.0 Unported)
What is biodiversity informatics?
How are biodiversity data used?
How are biodiversity data made available?
What are the k...
Bioinformatics
focused on the *omics
Biodiversity Informatics
interoperability of scientific
names, classifications
History of “Biodiversity Informatics”
John S. Whiting
Canadian Biodiversity
Informatics Consortium (1993)
Johnson Norm F. 2007. Biodiversity
informatics. Annu Rev Entomol. 52:421-38.
DOI 10.1146/annurev.ento.52.110405.091259
Who, What,
Where, When?
How are biodiversity data used?
Chapman, A. D. 2005. Uses of Primary
Species-Occurrence Data, version 1.0.
Report for the Global Biodiversity
Information ...
1 Taxonomy:
research, indices, floras/faunas, field
guides, phylogenies
2 Biogeography: distributional atlases, species
di...
Uses of Primary Occurrence Data
8 Conservation Planning: rapid biodiversity
assessments, identifying priority areas, reser...
DOI 10.7717/peerj.11
DOI 10.1038/nature12872
How are biodiversity data made
available?
The Process
Collect
Prepare
Digitize
Standardize
Publish
Collect
© Ainsley Seago
Prepare
Creating a long-term voucher
for scientific research
Specimen label
Primary biodiversity data
What, when, where & who
Digitize
Recording specimen information
in a digital format
Standardize
Different database systems
Different formats
Different languages
Darwin Core
A common biodiversity
information language
bit.ly/DarwinCore
175 terms
Darwin Core Archive
A common biodiversity
information format
Publish
Make available online
GBIF Integrated Publishing Toolkit (IPT)
What Other Kinds of Data?
Images
Observations
Phylogenetic Trees
Graphs
Unstructured texts
Taxonomic lists
What are the key challenges?
Scientific Names
DOI 10.1007/11530084_8
Homonyms
same name for many taxa
Synonyms
different names for same taxa
Variant representations
orthography, spelling,
dif...
DOI 10.1016/j.tree.2010.09.004
Globally Unique Identifiers
Data Quality and Fitness-for-Use
Giving Credit for Participation &
Metrics of Success
What are (a few of) the Biodiversity
Informatics organizations?
*.globalnames.org
Edit
http://gnite.org
Index
http://gni.*
Atomize
…{
genus: { epitheton: "Pardosa" },
species: {
basionym...
What about Canadian Organizations?
Federal Biodiversity Information Partnership
Canadian Biodiversity Information Facility...
canadensys.net
Academic
11 universities, 5 botanical
gardens & 2 museums
35+ researchers
30 collections
Plants, insects and fungi
Canadensys Headquarters
Université de Montréal
Biodiversity Centre
13 mil. specimens
2 out of 3 are insects
Goal
Mobilize 3 million specimen
records (20%)
Download
Per dataset
Not very flexible
Checklists
Data about taxa (vs specimens)
also supported by
DwC-A, GBIF & IPT
VASCAN
Database of Vascular Plants of Canada
data.canadensys.net/vascan
Biological Survey of Canada
The Biota of Canada
http://www.biologicalsurvey.ca
Data license
Allow data to be used
bit.ly/cc0-for-data
Where can I go for more?
Social Venues
TAXACOM
TDWG
Canadensys Google Group
iDigBio
ECN-L
GitHub
Twitter
What Skills/Technologies
Might I Need?
Web programming: HTML5, css
Relational databases: PostgreSQL/PostGIS,
MySQL
NoSQL d...
Biodiversity Informatics
Commercialization
iekho.com
Branché
What is biodiversity informatics?
How are biodiversity data used?
How are biodiversity data made available?
What are the k...
www.canadensys.net
@canadensys
@dpsSpiders
david.shorthouse@umontreal.ca
David P. Shorthouse
2014.04.01 Shorthouse REDM400
2014.04.01 Shorthouse REDM400
2014.04.01 Shorthouse REDM400
2014.04.01 Shorthouse REDM400
2014.04.01 Shorthouse REDM400
2014.04.01 Shorthouse REDM400
2014.04.01 Shorthouse REDM400
2014.04.01 Shorthouse REDM400
2014.04.01 Shorthouse REDM400
2014.04.01 Shorthouse REDM400
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2014.04.01 Shorthouse REDM400

  1. 1. Biodiversity Informatics David P. Shorthouse, Université de Montréal
  2. 2. © Mr.checker (CC-SA 3.0 Unported)
  3. 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. 4. Bioinformatics focused on the *omics
  5. 5. Biodiversity Informatics interoperability of scientific names, classifications
  6. 6. History of “Biodiversity Informatics” John S. Whiting Canadian Biodiversity Informatics Consortium (1993)
  7. 7. Johnson Norm F. 2007. Biodiversity informatics. Annu Rev Entomol. 52:421-38. DOI 10.1146/annurev.ento.52.110405.091259
  8. 8. Who, What, Where, When?
  9. 9. How are biodiversity data used?
  10. 10. 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
  11. 11. 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
  12. 12. 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
  13. 13. DOI 10.7717/peerj.11
  14. 14. DOI 10.1038/nature12872
  15. 15. How are biodiversity data made available?
  16. 16. The Process Collect Prepare Digitize Standardize Publish
  17. 17. Collect © Ainsley Seago
  18. 18. Prepare Creating a long-term voucher for scientific research
  19. 19. Specimen label Primary biodiversity data What, when, where & who
  20. 20. Digitize Recording specimen information in a digital format
  21. 21. Standardize Different database systems Different formats Different languages
  22. 22. Darwin Core A common biodiversity information language bit.ly/DarwinCore
  23. 23. 175 terms
  24. 24. Darwin Core Archive A common biodiversity information format
  25. 25. Publish Make available online GBIF Integrated Publishing Toolkit (IPT)
  26. 26. What Other Kinds of Data? Images Observations Phylogenetic Trees Graphs Unstructured texts Taxonomic lists
  27. 27. What are the key challenges?
  28. 28. Scientific Names
  29. 29. DOI 10.1007/11530084_8
  30. 30. Homonyms same name for many taxa Synonyms different names for same taxa Variant representations orthography, spelling, differences in authority
  31. 31. DOI 10.1016/j.tree.2010.09.004
  32. 32. Globally Unique Identifiers
  33. 33. Data Quality and Fitness-for-Use
  34. 34. Giving Credit for Participation & Metrics of Success
  35. 35. What are (a few of) the Biodiversity Informatics organizations?
  36. 36. *.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
  37. 37. What about Canadian Organizations? Federal Biodiversity Information Partnership Canadian Biodiversity Information Facility OBIS Canada
  38. 38. canadensys.net
  39. 39. Academic 11 universities, 5 botanical gardens & 2 museums 35+ researchers
  40. 40. 30 collections Plants, insects and fungi
  41. 41. Canadensys Headquarters Université de Montréal Biodiversity Centre
  42. 42. 13 mil. specimens 2 out of 3 are insects
  43. 43. Goal Mobilize 3 million specimen records (20%)
  44. 44. Download Per dataset Not very flexible
  45. 45. Checklists Data about taxa (vs specimens) also supported by DwC-A, GBIF & IPT
  46. 46. VASCAN Database of Vascular Plants of Canada data.canadensys.net/vascan
  47. 47. Biological Survey of Canada The Biota of Canada http://www.biologicalsurvey.ca
  48. 48. Data license Allow data to be used bit.ly/cc0-for-data
  49. 49. Where can I go for more?
  50. 50. Social Venues TAXACOM TDWG Canadensys Google Group iDigBio ECN-L GitHub Twitter
  51. 51. 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
  52. 52. Biodiversity Informatics Commercialization iekho.com Branché
  53. 53. 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?
  54. 54. www.canadensys.net @canadensys @dpsSpiders david.shorthouse@umontreal.ca David P. Shorthouse

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