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 ...
Bioinformaticsfocused on the *omics
Biodiversity Informaticsinteroperability of scientific names,          classifications
History of “Biodiversity Informatics”                           Canadian Biodiversity                      Informatics Con...
Johnson Norm F. 2007. Biodiversity                 informatics. Annu Rev Entomol. 52:421-38.DOI 10.1146/annurev.ento.52.11...
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 Fac...
Uses of Primary Occurrence Data1 Taxonomy: research, indices, floras/faunas, field guides,  phylogenies2 Biogeography: dis...
Uses of Primary Occurrence Data9 Health and Public Safety: disease and disease   vectors, bioterrorism, biosafety, parasit...
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 richa...
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      ...
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,diff...
What are (a few of) the Biodiversity   Informatics organizations?
Global Names  Find                        Atomize                                    Index                       …{       ...
Applying Global Names Tools                             80                             70                             60  ...
What about Canadian Organizations?  Federal Biodiversity Information Partnership  Canadian Biodiversity Information Facili...
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 ...
Thanks!        www.canadensys.net           @canadensys           @dpsSpiders  david.shorthouse@umontreal.caDavid P. Short...
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
Introduction to Biodiversity Informatics
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Introduction to Biodiversity Informatics

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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

    1. 1. Biodiversity InformaticsDavid P. Shorthouse, Université de Montréal
    2. 2. TrochosaterricolaThorell, 1856 Trochosaruricola(De Geer, 1778)
    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. Bioinformaticsfocused on the *omics
    5. 5. Biodiversity Informaticsinteroperability of scientific names, classifications
    6. 6. History of “Biodiversity Informatics” Canadian Biodiversity Informatics Consortium (1993) John S. Whiting
    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. http://www.simplemappr.net
    10. 10. How are biodiversity data used?
    11. 11. Chapman, A. D. 2005. Uses of PrimarySpecies-Occurrence Data, version 1.0.Report for the Global BiodiversityInformation Facility, Copenhagen.
    12. 12. 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
    13. 13. 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
    14. 14. DOI 10.7717/peerj.11
    15. 15. Dr. Jeremy Kerr, University of Ottawa
    16. 16. How are biodiversity data made available?
    17. 17. The Process Collect Prepare Digitize Standardize Publish
    18. 18. CollectWhy do we collect specimens?
    19. 19. PrepareCreating a long-term voucher for scientific research
    20. 20. Specimen labelPrimary biodiversity dataWhat, when, where & who
    21. 21. 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
    22. 22. When?Date -> trends
    23. 23. Where?Locality, elevation & habitat
    24. 24. GeoreferencingLocality description -> Coordinates
    25. 25. Who?Collector -> history
    26. 26. Locked in paper format Not easily accessible
    27. 27. DigitizeRecording specimen information in a digital format
    28. 28. StandardizeDifferent database systems Different formats Different languages
    29. 29. Darwin CoreA common biodiversity information language bit.ly/DarwinCore
    30. 30. 175 terms
    31. 31. Darwin Core Archive A common biodiversity information format
    32. 32. Simplify Standardize Harvest & publish Tapir protocol GBIF’sDatabase central index DarwinCore Archive User
    33. 33. Publish Make available onlineGBIF Integrated Publishing Toolkit (IPT)
    34. 34. What are the key challenges?
    35. 35. DOI 10.1016/j.tree.2010.09.004
    36. 36. DOI 10.1007/11530084_8
    37. 37. Homonymssame name for many taxaSynonyms different names for same taxaVariant representations orthography, spelling,differences in authority
    38. 38. What are (a few of) the Biodiversity Informatics organizations?
    39. 39. 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
    40. 40. 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
    41. 41. What about Canadian Organizations? Federal Biodiversity Information Partnership Canadian Biodiversity Information Facility OBIS Canada
    42. 42. canadensys.net
    43. 43. A networkOf people and collections
    44. 44. Academic11 universities, 5 botanical gardens & 2 museums
    45. 45. Canadensys HeadquartersUniversité de MontréalBiodiversity Centre
    46. 46. 35+ researchers Mainly systematists
    47. 47. 30 collectionsPlants, insects and fungi
    48. 48. 13 mil. specimens 2 out of 3 are insects
    49. 49. GoalMobilize 3 million specimen records (20%) by 2013
    50. 50. Carole SinouData Publication Support Professional
    51. 51. Download Per datasetNot very flexible
    52. 52. ChecklistsData about taxa (vs specimens) Now also supported by DwC-A, GBIF & IPT
    53. 53. VASCANDatabase of Vascular Plants of Canada data.canadensys.net/vascan
    54. 54. Data licenseAllow data to be used bit.ly/cc0-for-data
    55. 55. Where can I go for more?
    56. 56. Biodiversity Informatics Commercialization
    57. 57. 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?
    58. 58. Thanks! www.canadensys.net @canadensys @dpsSpiders david.shorthouse@umontreal.caDavid P. Shorthouse
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