2014.04.01 Shorthouse REDM400
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Transcript of 2014.04.01 Shorthouse REDM400
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Biodiversity Informatics
David P. Shorthouse, Université de Montréal
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© Mr.checker (CC-SA 3.0 Unported)
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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?
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Bioinformaticsfocused on the *omics
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Biodiversity Informaticsinteroperability of scientific names,
classifications
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History of “Biodiversity Informatics”
John S. Whiting
Canadian BiodiversityInformatics Consortium (1993)
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Johnson Norm F. 2007. Biodiversity informatics. Annu Rev Entomol. 52:421-38.
DOI 10.1146/annurev.ento.52.110405.091259
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Who, What,Where, When?
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How are biodiversity data used?
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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
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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
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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
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DOI 10.7717/peerj.11
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DOI 10.1038/nature12872
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How are biodiversity data made available?
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The Process
CollectPrepareDigitizeStandardizePublish
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Collect
© Ainsley Seago
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PrepareCreating a long-term voucher
for scientific research
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Specimen labelPrimary biodiversity data
What, when, where & who
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DigitizeRecording specimen information
in a digital format
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StandardizeDifferent database systems
Different formatsDifferent languages
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175 terms
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Darwin Core ArchiveA common biodiversity
information format
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PublishMake available online
GBIF Integrated Publishing Toolkit (IPT)
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What Other Kinds of Data?
ImagesObservationsPhylogenetic TreesGraphsUnstructured textsTaxonomic lists
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What are the key challenges?
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Scientific Names
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DOI 10.1007/11530084_8
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Homonymssame name for many taxa
Synonymsdifferent names for same taxa
Variant representationsorthography, spelling,differences in authority
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DOI 10.1016/j.tree.2010.09.004
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Globally Unique Identifiers
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Data Quality and Fitness-for-Use
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Giving Credit for Participation & Metrics of Success
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What are (a few of) the Biodiversity Informatics organizations?
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*.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
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What about Canadian Organizations?
Federal Biodiversity Information PartnershipCanadian Biodiversity Information FacilityOBIS Canada
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canadensys.net
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Academic11 universities, 5 botanical
gardens & 2 museums35+ researchers
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30 collectionsPlants, insects and fungi
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Canadensys HeadquartersUniversité de MontréalBiodiversity Centre
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13 mil. specimens2 out of 3 are insects
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GoalMobilize 3 million specimen
records (20%)
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DownloadPer dataset
Not very flexible
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ChecklistsData about taxa (vs specimens)
also supported byDwC-A, GBIF & IPT
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VASCANDatabase of Vascular Plants of Canada
data.canadensys.net/vascan
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Biological Survey of CanadaThe Biota of Canada
http://www.biologicalsurvey.ca
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Where can I go for more?
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Social Venues
TAXACOMTDWGCanadensys Google GroupiDigBioECN-LGitHubTwitter
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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
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Biodiversity Informatics Commercialization
iekho.comBranché
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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?
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www.canadensys.net@canadensys@dpsSpiders
David P. Shorthouse