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Biodiversity Informatics
David P. Shorthouse, Université de Montréal
Trochosa ruricola (De Geer, 1778)Trochosa terricola Thorell, 1856
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?
Bioinformaticsfocused on the *omics
Biodiversity Informaticsinteroperability of scientific names,
classifications
History of “Biodiversity Informatics”
John S. Whiting
Canadian BiodiversityInformatics 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?
http://www.simplemappr.net
How are biodiversity data used?
Chapman, A. D. 2005. Uses of Primary Species-Occurrence Data, version 1.0. Report for the Global Biodiversity Information Facility, Copenhagen.
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 Phenologies4 Endangered, Migratory, and Invasive Species5 Impact of Climate Change6 Ecology, Evolution and Genetics: habitat loss, ecosystem
function7 Environmental Planning: impact assessments8 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 Bioprospecting11 Border Control and Wildlife Trade12 Education and Public Outreach13 Ecotourism14 Society and Politics: data repatriation15 Recreational activities
Uses of Primary Occurrence Data
DOI 10.7717/peerj.11
Dr. Jeremy Kerr, University of Ottawa
How are biodiversity data made available?
The Process
CollectPrepareDigitizeStandardizePublish
CollectWhy do we collect specimens?
PrepareCreating a long-term voucher
for scientific research
Specimen labelPrimary biodiversity data
What, when, where & who
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• Eriophorum scheuchzeri• Festuca altaica• Huperzia haleakalae
When?Date -> trends
Where?Locality, elevation & habitat
GeoreferencingLocality description -> Coordinates
Who?Collector -> history
Locked in paper formatNot easily accessible
DigitizeRecording specimen information
in a digital format
StandardizeDifferent database systems
Different formatsDifferent languages
175 terms
Darwin Core ArchiveA common biodiversity
information format
Database
DarwinCoreArchive
Tapir protocol
Standardize & publish
GBIF’scentral index
Harvest
User
Simplify
PublishMake available online
GBIF Integrated Publishing Toolkit (IPT)
What are the key challenges?
DOI 10.1016/j.tree.2010.09.004
DOI 10.1007/11530084_8
Homonymssame name for many taxa
Synonymsdifferent names for same taxa
Variant representationsorthography, spelling,differences in authority
What are (a few of) the Biodiversity Informatics organizations?
*.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
Applying Global Names Tools
# N
ames
foun
d
Data Packages Published PDF0
10
20
30
40
50
60
70
t220 =, 3.68 p = 0.0003
Coming Soon
What about Canadian Organizations?
Federal Biodiversity Information PartnershipCanadian Biodiversity Information FacilityOBIS Canada
canadensys.net
A networkOf people and collections
Academic11 universities, 5 botanical
gardens & 2 museums
Canadensys HeadquartersUniversité de MontréalBiodiversity Centre
35+ researchersMainly systematists
30 collectionsPlants, insects and fungi
13 mil. specimens2 out of 3 are insects
GoalMobilize 3 million specimen
records (20%) by 2013
Carole SinouData Publication Support Professional
DownloadPer dataset
Not very flexible
ChecklistsData about taxa (vs specimens)
Now also supported byDwC-A, GBIF & IPT
VASCANDatabase of Vascular Plants of Canada
data.canadensys.net/vascan
Where can I go for more?
Biodiversity Informatics Commercialization
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?
Thanks!www.canadensys.net
@canadensys@dpsSpiders
David P. Shorthouse