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Scratchpads

Scratchpads. The virtual research environment for biodiversity data. Simon Rycroft , Dave Roberts, Vince Smith , Alice Heaton, Katherine Bouton , Laurence Livermore , Dimitris Koureas , Ed Baker Natural History Museum, London. What are Scratchpads?.

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Scratchpads

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  1. Scratchpads The virtual research environment for biodiversity data Simon Rycroft, Dave Roberts, Vince Smith, Alice Heaton, Katherine Bouton, Laurence Livermore, DimitrisKoureas, Ed Baker Natural History Museum, London

  2. What are Scratchpads? Hosted websites for biodiversity data Virtual research & publication platform Completely open access & open source Modular & flexible

  3. A Scratchpad is a website that holds data for you and your community The Scratchpads concept External data & services Your data

  4. Examples of use: Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies

  5. Major integrated project • 21+ open community sites and growing • Over 45 internationally collaborating scientists • Site data feeds into a “Portal” Site List: http://about.e-monocot.org/list-emonocot-scratchpads

  6. Major integrated project • Retrieve information on any Monocot plant • Rich downloadable data • Identification keys • Model example of linked attributed data eMonocot Portal: http://e-monocot.org/

  7. The main features Dynamic Biological Classifications Manually entered or imported Auto generated

  8. The main features Taxon pages Overview of data related to taxon Generated from tagged content

  9. The main features Bibliography management An inbuilt Bibliography manager Faceted browsing Taxon tagging and free keywords Import from and export to all major formats

  10. The main features Specimen/Observation data Annotated full specimen/observation records Linked to images and georeferenced Linked to GenBank accession numbers

  11. The main features Distribution maps Google maps based Data layers Occurrence data Distribution data TDWG regions GBIF data

  12. Example regional distribution The main features

  13. Create phylogenetic trees Based on Newick/NeXML Different views

  14. The main features Character matrices – Key construction Quantitative or qualitative characters Auto generation of keys Taxon based matrices [Specimens based character matrices]

  15. The main features Media handling Bulk upload Metadata (EXIF & Audubon core) Media galleries

  16. The main features Generation of custom pages Tagged or not External RSS Twitter feeds Media files

  17. The main features Enhanced communication tools Working groups Forums Blog entries Webforms Newsletters RSS syndication Inbuilt comments

  18. External services Integration data mobilisation more on the way…

  19. IUCN data integration

  20. GBIF distribution data integration

  21. Structured data Select, describe & annotate data Publication module Publish, cite, disseminate & archive data Major repositories

  22. Scratchpads Publication Module • Scratchpads templates for publishing... • Taxon treatments • Nomenclatural acts • Checklists / inventories • Identification keys and trees • Metadata descriptions of databases • Descriptions of software tools • Easy & intuitive • Draws on data from your site • Pre-submission validation • Submitted as structured XML • No reformatting

  23. Are Scratchpads sustainable? 590 Scratchpads Communities by 6,800 active registered users covering 91,631 taxa in 570,000 pages. In total more than1,500,000 unique visitors Per month unique visitors to Scratchpads sites 65,000 visitors/month

  24. Are Scratchpads sustainable? 2011 2007 2014 ViBRANT Virtual Biodiversity Research & & Other grants in the pipeline Horizon 2020

  25. About scratchpads.eu Code git.scratchpads.eu Try sandbox.scratchpads.eu

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