Scratchpads: the Virtual Research Environment for biodiversity data


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Rycroft, S., Roberts, D., Smith, V., Heaton, A., Bouton, K., Livermore, L., Koureas, D., Baker, E. 2013. Scratchpads: the Virtual Research Environment for biodiversity data. TDWG, Biodiversity Information Standards. Grand Hotel Mediterraneo Florence, Italy, 27 Oct - 1 Nov., 2013.

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  • In the project there are more than 21 eMonocot Scratchpads which have over 45 international collaborating scientists.The eMonocot Scratchpads cover over 15 families with more planned with additional workshops which will take place this year at Monocots V in New York.The Scratchpad to eMonocot Portal link is now active and available for the public to browse all the Scratchpad data combined with other external monocot resources.
  • All of the information is brought together in the eMonocot portal. The information presented here will be especially useful for anyone studying the ecology or evolution of the monocot plants, or who wants to understand monocot biodiversity and conservation.The portal provides taxon descriptions, distribution maps, taxonomies and keys, all of which are downloadable and attributed to the author and contributing site.
  • Intuitive professional looking layout.Easy to compile taxon pages without any knowledge of web design.Taxonomy provides the crucial backbone, linking content together and is easily updateable.On this page you can see the classification browser in the side bar, detailed nomenclatural information, images and a diagnostic summary.
  • The Scratchpad Publication Module fixes that by allowing you to select your structured data, describe it an annotate in an easy-to-use manuscript template and submit this to Pensoft Publishers for formal publication online as a peer-reviewed article.Your paper is then citable, widely disseminated to major services and data aggregators and all the data archived.
  • The Scratchpads Publication Module
  • Scratchpads: the Virtual Research Environment for biodiversity data

    1. 1. 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
    2. 2. What are Scratchpads? • Hosted websites for biodiversity data • Virtual research & publication platform • Completely open access & open source • Modular & flexible
    3. 3. The Scratchpads concept A Scratchpad is a website that holds data for you and your community Your data External data & services
    4. 4. Examples of use: Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies
    5. 5. Major integrated project • 21+ open community sites and growing • Over 45 internationally collaborating scientists • Site data feeds into a “Portal” Site List:
    6. 6. Major integrated project • Retrieve information on any Monocot plant • Rich downloadable data • Identification keys • Model example of linked attributed data eMonocot Portal:
    7. 7. The main features Dynamic Biological Classifications Manually entered or imported Auto generated
    8. 8. The main features Taxon pages Overview of data related to taxon Generated from tagged content
    9. 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. 10. The main features Specimen/Observation data Annotated full specimen/observation records Linked to images and georeferenced Linked to GenBank accession numbers
    11. 11. The main features Distribution maps Google maps based Data layers Occurrence data Distribution data TDWG regions GBIF data
    12. 12. The main features Example regional distribution
    13. 13. Create phylogenetic trees Based on Newick/NeXML Different views
    14. 14. The main features Character matrices – Key construction Quantitative or qualitative characters Auto generation of keys Taxon based matrices [Specimens based character matrices]
    15. 15. The main features Media handling Bulk upload Metadata (EXIF & Audubon core) Media galleries
    16. 16. The main features Generation of custom pages Tagged or not External RSS Twitter feeds Media files
    17. 17. The main features Enhanced communication tools Working groups Forums Blog entries Webforms Newsletters RSS syndication Inbuilt comments
    18. 18. External services Integration data mobilisation more on the way…
    19. 19. IUCN data integration
    20. 20. GBIF distribution data integration
    21. 21. Structured data Select, describe & annotate data Publication module Publish, cite, disseminate & archive data Major repositories
    22. 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. 23. Are Scratchpads sustainable? 590 Scratchpads Communities by 6,800 active registered users covering 91,631 taxa in 570,000 pages. In total more than 1,500,000 unique visitors Per month unique visitors to Scratchpads sites 65,000 visitors/month
    24. 24. Are Scratchpads sustainable? 2007 2011 2014 ViBRANT Virtual Biodiversity Research & & Other grants in the pipeline Horizon 2020
    25. 25. About Code Try