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Canadensys
    A Network for Mobilizing Primary
        Biodiversity Knowledge




David Shorthouse, Christian Gendreau
Canadensys Headquarters
Université de Montréal
Biodiversity Centre
Network
11 universities, 2 botanical gardens, 2
               museums
Goal
Mobilize 3 million specimen
records (20%) by end 2013
Canadensys Processes
http://www.canadensys.net
https://github.com/Canadensys
Carole Sinou
Data Publication Support Professional
Canadensys Products
Where = georeferencing
What = species identity
readraw data
               narwhal-
                                          DarwinCore
Processing    processor
                                           Archive
                     insert data

                             pull from
                PostgreSQL
Searchable data                           ElasticSearch
                 PostGIS

                          query
             Canadensys
Web app                            Windshaft
              Explorer
narwhal-processor
 Goal Standardize data for optimal retrieval
 • Geography (continent, country, coordinates …)
 • Dates (different formats, partial dates)
 • Numerics (allowintervalsearch)
 • Scientificnames (atomize, aggregate)
Geospatialstack



  Windshaft          Mapnik 2.1        Postgis 2.0
  • Nodejs           • Map render      • Handles
    TileServer       • Used by           complex
  • Made by            OpenStreetMap     geospatial
    Vizzuality and                       query
    OpenSource                         • Allow clustering
Integrate Publishing Toolkit 2.0.4
 • http://code.google.com/p/gbif-providertoolkit/
 • Permits management, administration, publishing of
   occurrence, checklist, metadata resources
    – Create metadata (Ecological Metadata Language, eml.xml)
    – Map resource to DarwinCore and optional extensions
 • Register resources with GBIF
 • RSS feed for changes (eg updates) in resources
Limulus
                                  polyphemus
 Kiwa
hirsuta
                            Trypanosoma
                                   brucei
      Aa
      aleacea

                 Homo sapiens
                                               Pieris
                                               rapae


                                               Pieris
                                               japponica

Osedax            Bahumbugi
frankpressi
                Kingiaaustralis
The problem with scientific names

 •   No comprehensive catalog of species
 •   Names ≠ species
 •   The species problem – species concepts
 •   Competing classifications / phylogenies
 •   Many names for one taxon
 •   One name for many taxa
 •   ‘Names’ are more than code-compliant scientific names
A working solution
 • Inclusive
    – Accommodate alternate perspectives
 • Reconciliation
    – Map names among and between each other
 • Disambiguation
    – Context to assign homonymic names to rightful place
Current Activities
Proposition
www.canadensys.net
    david.shorthouse@umontreal.ca
   christian.gendreau@umontreal.ca
              @canadensys



David Shorthouse, Christian Gendreau

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Canadensys - Federal Geospatial Platform

  • 1. Canadensys A Network for Mobilizing Primary Biodiversity Knowledge David Shorthouse, Christian Gendreau
  • 2. Canadensys Headquarters Université de Montréal Biodiversity Centre
  • 3. Network 11 universities, 2 botanical gardens, 2 museums
  • 4. Goal Mobilize 3 million specimen records (20%) by end 2013
  • 7.
  • 8. Carole Sinou Data Publication Support Professional
  • 10.
  • 11. Where = georeferencing What = species identity
  • 12.
  • 13.
  • 14.
  • 15. readraw data narwhal- DarwinCore Processing processor Archive insert data pull from PostgreSQL Searchable data ElasticSearch PostGIS query Canadensys Web app Windshaft Explorer
  • 16. narwhal-processor Goal Standardize data for optimal retrieval • Geography (continent, country, coordinates …) • Dates (different formats, partial dates) • Numerics (allowintervalsearch) • Scientificnames (atomize, aggregate)
  • 17. Geospatialstack Windshaft Mapnik 2.1 Postgis 2.0 • Nodejs • Map render • Handles TileServer • Used by complex • Made by OpenStreetMap geospatial Vizzuality and query OpenSource • Allow clustering
  • 18. Integrate Publishing Toolkit 2.0.4 • http://code.google.com/p/gbif-providertoolkit/ • Permits management, administration, publishing of occurrence, checklist, metadata resources – Create metadata (Ecological Metadata Language, eml.xml) – Map resource to DarwinCore and optional extensions • Register resources with GBIF • RSS feed for changes (eg updates) in resources
  • 19. Limulus polyphemus Kiwa hirsuta Trypanosoma brucei Aa aleacea Homo sapiens Pieris rapae Pieris japponica Osedax Bahumbugi frankpressi Kingiaaustralis
  • 20. The problem with scientific names • No comprehensive catalog of species • Names ≠ species • The species problem – species concepts • Competing classifications / phylogenies • Many names for one taxon • One name for many taxa • ‘Names’ are more than code-compliant scientific names
  • 21. A working solution • Inclusive – Accommodate alternate perspectives • Reconciliation – Map names among and between each other • Disambiguation – Context to assign homonymic names to rightful place
  • 24. www.canadensys.net david.shorthouse@umontreal.ca christian.gendreau@umontreal.ca @canadensys David Shorthouse, Christian Gendreau

Editor's Notes

  1. Integrated Publishing Toolkit: Occurrence and Checklist DataExplorer