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Introduction to Biodiversity Informatics

Introduction to Biodiversity Informatics



Delivered Apr 2, 2013 at Redpath Museum auditorium, McGill University for Science and Museums, REDM400

Delivered Apr 2, 2013 at Redpath Museum auditorium, McGill University for Science and Museums, REDM400



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  • it aids in sequencing and annotating genomes and their observed mutations.Aids in development of biological and gene ontologies to organize and query biological dataplays a role in the analysis of gene and protein expression and regulation
  • computerized handling of any biodiversity informationIt typically builds on a foundation of taxonomic, biogeographic, or ecological information stored in digital form, which, with the application of modern computer techniques, can yield new ways to view and analyse existing information, as well as predictive models for information that does not yet exist
  • Coined by John Whiting in 1992 to cover the activities of an entity known as the Canadian Biodiversity Informatics Consortium, a group involved with fusing basic biodiversity information with environmental economics and geospatial information in the form of GPS and GIS.I coined the term as part of a title for what was at first a loose affiliation between about five agencies (including myself, a firm specializing in GPS, and GIS firm, a firm specializing in database management, a firm specializing in environmental economics, and a representative of the Canadian Museum of Naturelost any obligate connection with the GPS/GIS world and be associated with the computerized management of any aspects of biodiversity information
  • Biodiversity Informatics – 2004

Introduction to Biodiversity Informatics Introduction to Biodiversity Informatics Presentation Transcript

  • Biodiversity InformaticsDavid P. Shorthouse, Université de Montréal
  • TrochosaterricolaThorell, 1856 Trochosaruricola(De Geer, 1778)
  • 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” Canadian Biodiversity Informatics Consortium (1993) John S. Whiting
  • 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 PrimarySpecies-Occurrence Data, version 1.0.Report for the Global BiodiversityInformation Facility, Copenhagen.
  • Uses of Primary Occurrence Data1 Taxonomy: research, indices, floras/faunas, field guides, phylogenies2 Biogeography: distributional atlases, species distribution modeling, species decline3 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
  • Uses of Primary Occurrence Data9 Health and Public Safety: disease and disease vectors, bioterrorism, biosafety, parasitology10 Bioprospecting11 Border Control and Wildlife Trade12 Education and Public Outreach13 Ecotourism14 Society and Politics: data repatriation15 Recreational activities
  • DOI 10.7717/peerj.11
  • Dr. Jeremy Kerr, University of Ottawa
  • How are biodiversity data made available?
  • The Process Collect Prepare Digitize Standardize Publish
  • CollectWhy do we collect specimens?
  • PrepareCreating a long-term voucher for scientific research
  • Specimen labelPrimary biodiversity dataWhat, 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
  • When?Date -> trends
  • Where?Locality, elevation & habitat
  • GeoreferencingLocality description -> Coordinates
  • Who?Collector -> history
  • Locked in paper format Not easily accessible
  • DigitizeRecording specimen information in a digital format
  • StandardizeDifferent database systems Different formats Different languages
  • Darwin CoreA common biodiversity information language bit.ly/DarwinCore
  • 175 terms
  • Darwin Core Archive A common biodiversity information format
  • Simplify Standardize Harvest & publish Tapir protocol GBIF’sDatabase central index DarwinCore Archive User
  • Publish Make available onlineGBIF 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 taxaSynonyms different names for same taxaVariant representations orthography, spelling,differences in authority
  • What are (a few of) the Biodiversity Informatics organizations?
  • Global Names Find Atomize Index …{ genus: { epitheton: "Pardosa" }, species: { basionymAuthorTeam: { year: "1892”, authorTeam: "Banks", author: ["Banks”] }, epitheton: "moesta", authorship: "Banks, 1892" } http://gni.* }…http://gnrd.* Resolve Edit http://gnite.org http://resolver.* *.globalnames.org
  • Applying Global Names Tools 80 70 60 # Names found 50 40 30 20 t220 =, 3.68 p = 0.0003 10 0 Data Packages Published PDF
  • What about Canadian Organizations? Federal Biodiversity Information Partnership Canadian Biodiversity Information Facility OBIS Canada
  • canadensys.net
  • A networkOf people and collections
  • Academic11 universities, 5 botanical gardens & 2 museums
  • Canadensys HeadquartersUniversité de MontréalBiodiversity Centre
  • 35+ researchers Mainly systematists
  • 30 collectionsPlants, insects and fungi
  • 13 mil. specimens 2 out of 3 are insects
  • GoalMobilize 3 million specimen records (20%) by 2013
  • Carole SinouData Publication Support Professional
  • Download Per datasetNot very flexible
  • ChecklistsData about taxa (vs specimens) Now also supported by DwC-A, GBIF & IPT
  • VASCANDatabase of Vascular Plants of Canada data.canadensys.net/vascan
  • Data licenseAllow data to be used bit.ly/cc0-for-data
  • 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.shorthouse@umontreal.caDavid P. Shorthouse