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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 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?
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.
http://www.gbif.org/resources/2834
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 assessments
Uses of Primary Occurrence Data
Uses of Primary Occurrence Data8 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
DOI 10.7717/peerj.11
DOI 10.1038/nature12872
How are biodiversity data made available?
The Process
CollectPrepareDigitizeStandardizePublish
Collect
© Ainsley Seago
PrepareCreating a long-term voucher
for scientific research
Specimen labelPrimary biodiversity data
What, when, where & who
DigitizeRecording specimen information
in a digital format
StandardizeDifferent database systems
Different formatsDifferent languages
175 terms
Darwin Core ArchiveA common biodiversity
information format
PublishMake available online
GBIF Integrated Publishing Toolkit (IPT)
What Other Kinds of Data?
ImagesObservationsPhylogenetic TreesGraphsUnstructured textsTaxonomic lists
What are the key challenges?
Scientific Names
DOI 10.1007/11530084_8
Homonymssame name for many taxa
Synonymsdifferent names for same taxa
Variant representationsorthography, spelling,differences in authority
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: { basionymAuthorTeam: { year: "1892”, authorTeam: "Banks", author: ["Banks”] }, epitheton: "moesta", authorship: "Banks, 1892" }}…
Resolve
http://resolver.*
Find
http://gnrd.*
Global Names
What about Canadian Organizations?
Federal Biodiversity Information PartnershipCanadian Biodiversity Information FacilityOBIS Canada
canadensys.net
Academic11 universities, 5 botanical
gardens & 2 museums35+ researchers
30 collectionsPlants, insects and fungi
Canadensys HeadquartersUniversité de MontréalBiodiversity Centre
13 mil. specimens2 out of 3 are insects
GoalMobilize 3 million specimen
records (20%)
DownloadPer dataset
Not very flexible
ChecklistsData about taxa (vs specimens)
also supported byDwC-A, GBIF & IPT
VASCANDatabase of Vascular Plants of Canada
data.canadensys.net/vascan
Biological Survey of CanadaThe Biota of Canada
http://www.biologicalsurvey.ca
Where can I go for more?
Social Venues
TAXACOMTDWGCanadensys Google GroupiDigBioECN-LGitHubTwitter
What Skills/Technologies Might I Need?
Web programming: HTML5, cssRelational databases: PostgreSQL/PostGIS, MySQLNoSQL data stores: Neo4j, CouchDBProgramming languages: R, Python, ruby, Java, JavaScriptCreativity with data: dynamic visualizations
Biodiversity Informatics Commercialization
iekho.comBranché
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?
www.canadensys.net@canadensys@dpsSpiders
David P. Shorthouse