Scratchpads in the Biodiversity
Informatics Landscape




D. Roberts, K. Harman, S. Rycroft & V. Smith
Nomenclators                            Checklists
                                                                       ...
EDIT Directions &
    European
  Distributed


     Challenges
  Institute of
   Taxonomy




1. Collaborative working
2. ...
Scratchpads: Rationale
                         Hosted web sites, with
                         tools for taxonomists


  ...
What is a Scratchpad?
A website for you & your community




     1                2                   3
                 ...
Your data
   DNA & Phylogenies
                           Specimens




                                Descriptions




 ...
Taxonomy backbone

•  Classification import from uBio
   Classification Bank
•  Import from tab delimited files in three
 ...
Auto tagging

•  Quick and easy
•  Data available immediately after upload
•  Works with any extra data that may be
   add...
Small pieces loosely joined

 Has many potential meanings:
   •  Joining contributors together to form
      communities
Small pieces loosely joined

 Has many potential meanings:
   •  Joining contributors together to form
      communities
 ...
Small pieces loosely joined

 Has many potential meanings:
   •  Joining contributors together to form
      communities
 ...
TapirLink provides
 specimens to GBIF
based on Darwincore
Common Drupal base
  means LifeDesk
modules will work with
   Scratchpads
Working with colleagues
 in Berlin, we’ll also be
  providing data to the
       EDIT CDM
Current Scratchpads
                                         Ants
                      Sites:  70+        Bees
          ...
Questions?
Scratchpads in the Biodiversity Informatics Landscape
Scratchpads in the Biodiversity Informatics Landscape
Scratchpads in the Biodiversity Informatics Landscape
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Scratchpads in the Biodiversity Informatics Landscape

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Roberts, D., Harman, K., Rycroft, S.D. & Smith, V.S. Stockholm Biodiversity Informatics Symposium 2008, Swedish Museum of Natural History, Stockholm, Sweden  1-4 December 2008.

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Scratchpads in the Biodiversity Informatics Landscape

  1. 1. Scratchpads in the Biodiversity Informatics Landscape D. Roberts, K. Harman, S. Rycroft & V. Smith
  2. 2. Nomenclators Checklists Biodiversity Molecular Phylogenetic Index Fungorum PESI: Databases ALA ZooBank Tree of Life ERMS CONABIO IPNI TreeBase Fauna Europea NCBI/EMBL/DDBJ CRIA (Brazil) (Kew/AUS/Harvard) CIPRES Euro+Med Plantbase CBoL IUCN ING ORBIS Barcode of Life SEEK AFD/APC/APUI WORMS Initiative OPAL NZOR Flora Europea DAISIE CoL (Sp2000& ITIS) iNaturalist ZooRecord Molecular Distribution Functions Name Functions CDM Functions GNOMA GNA (NameBank) (Nomenclatpr LifeWatch Architecture) uBio GBIF TDWG Scan / Mark/up PLAZI Note: Inotaxa there are 600 biodiversity Literature BHL projects listed by TDWG Morphological Functions Specimen Access Functions eFloras including most of the projects listed here. Bibliographic IPNI Inter-Institutional Institutional Descriptive / Identification Google Scholar classification Key2Nature EMu (=MOA) Synthesis Connotea IdentifyLife Recorder BCI EoL ViTaL BioCASE Scratchpads ISI GeoCASE CATE MaNIS MorphoBank Wikipedia Indicated a link yet to be realised A many-to-many relationship
  3. 3. EDIT Directions & European Distributed Challenges Institute of Taxonomy 1. Collaborative working 2. Publication & Accessibility 3. Adaptability to the internet age Business as usual is not an option.
  4. 4. Scratchpads: Rationale Hosted web sites, with tools for taxonomists Intended to encourage community building Unbranded, to encourage community identity Tools to facilitate structuring of data
  5. 5. What is a Scratchpad? A website for you & your community 1 2 3 Uploaded & Published & reviewed Your data tagged on your site
  6. 6. Your data DNA & Phylogenies Specimens Descriptions Images Literature
  7. 7. Taxonomy backbone •  Classification import from uBio Classification Bank •  Import from tab delimited files in three different formats •  Makes use of a core feature of Drupal
  8. 8. Auto tagging •  Quick and easy •  Data available immediately after upload •  Works with any extra data that may be added to a taxonomy (vernacular names, synonymy)
  9. 9. Small pieces loosely joined Has many potential meanings: •  Joining contributors together to form communities
  10. 10. Small pieces loosely joined Has many potential meanings: •  Joining contributors together to form communities •  Joining the data together that go towards forming a Scratchpad
  11. 11. Small pieces loosely joined Has many potential meanings: •  Joining contributors together to form communities •  Joining the data together that go towards forming a Scratchpad •  Joining Scratchpad content with the landscape of biodiversity informatics data on the web
  12. 12. TapirLink provides specimens to GBIF based on Darwincore
  13. 13. Common Drupal base means LifeDesk modules will work with Scratchpads
  14. 14. Working with colleagues in Berlin, we’ll also be providing data to the EDIT CDM
  15. 15. Current Scratchpads Ants Sites: 70+ Bees Beetles Users: 850+ Big-headed flies Birds Pages: 130k Blackflies Ciliates Since March 2007 Cockroaches Dragon Trees Dung Beetles False Buttonweed Flat worms Flies Foraminifera Fossil Insects Fungus Gnats Holometabola Leaf-miner Flies Lice Lichens of Bermuda Malvaceae Megalastrum ferns Milichiid flies Mosquitoes Mosses Nannotax fossils Nepticuloid moths Palms Pearl oysters Polychaete worms Scaleworms Stick insects Sulawesi Ferns Termites Triticid grasses Weevils Wood Ferns
  16. 16. Questions?

×