3. ViBRANT
Virtual Biodiversity
21st Century taxonomy
The challenge for modern taxonomists
Goal…
• Inventory the Earth’s species
• Document their relationships
• “Publish” & apply these data
Data set…
• 1.8 M described spp. (10M names)
• 300M pages (over last 250 years)
• 1.5-3B specimens
People…
• 4-6,000 scientists
• 30-40,000 “pro-amateurs”
• Many more citizen scientists?
4. ViBRANT
Virtual Biodiversity
The problem
Science is global
• It needs global standards
• Global workflows
• Cooperation of global players
Science is carried out “locally”
• By local scientists
• Being part of local infrastructures
• Having local funders
5. ViBRANT
Virtual Biodiversity
Towards a solution
The European Distributed Institute of Taxonomy
• A Network of Excellence (NoE)
• 29 leading European, North American,
& Russian natural history collections-based
institutions
• Circa 12M !, funded under EU FP6
• March 2006 - February 2011
Products…
• Funding
• Training & outreach
• Websites
• Integrated scientific activities
• Inventories
• Computer tools
6. ViBRANT
Virtual Biodiversity
Goal
“a scholarly communication system
that is intertwined with the pursuit of
natural history, rather than an after-
thought or annex”
7. ViBRANT
Virtual Biodiversity
What is a Scratchpad?
A website for you & your community
1 2 3
Your data Uploaded & “Published” & reviewed
tagged on your site
Fast Intuitive Fit for use
8. ViBRANT
Virtual Biodiversity
Scratchpads
Overview
• Hosted websites for taxonomists
• Research & publication platform
• Modular (Drupal) & flexible
• Supports the taxonomic workflow
• Bottom-up design, agile dev.
• Ecosystem of communities (330+)
• 7,350+ users (unpaid) from 2007
9. ViBRANT
Virtual Biodiversity
Scratchpad Application Form
Free to any individual or community
13. ViBRANT
Virtual Biodiversity
Sustaining Scratchpads
ViBRANT: Building on EDIT & the Scratchpads
“To set up the means, tools and infrastructure to produce a more rational
and a more effective framework for European Biodiversity research”
• A Virtual Research Environment (Scratchpads) where users can safely
store, share and manage their research information.
• Analytical services for users to build identification keys and
phylogenetic trees.
• A publication platform for users to automatically compile taxonomic
manuscripts from their research database.
• A portal for users to centrally access publicly accessible biodiversity
research information and literature.
• Training, support & sociological study, helping research communities to
use these tools and services.
• A standards compliant technical architecture that can be sustained by
the biodiversity research community.
14. ViBRANT
Virtual Biodiversity
ViBRANT logistics
• Starts December 2010 (36 months)
• Project website (http://vbrant.eu)
• Virtual Research Communities, CP-CSA, EU FP7
• !6.2M Euros (EU Contribution !4.75M)
• 17 Partners in 9 countries, 603 person months
Collaboration…
• ESFRI Projects: LifeWatch, ELIXIR & EMBRC
• GBIF - controlled vocabularies, nodes & observational data recording
• PESI, 4D4Life & related EU projects
• Encyclopedia of Life, Barcode of Life & Biodiversity Heritage Library
• South African National Biodiversity Institute & Atlas of living Australia
31. ViBRANT
Virtual Biodiversity
Scratchpad 2 faceted search
• Rapid content discovery
• Systematic browsing
• Content specific facet
display (e.g. biblo, media)
• Slickgrid filters for other
content types
32. ViBRANT
Virtual Biodiversity
Scratchpad 2 multimedia gallery
• New look
• Video support
• Faceted search & browse
• Embed YouTube &
Vimeo
33. ViBRANT
Virtual Biodiversity
Scratchpad 2 taxon pages
• Easy publishing to EOL
• Better content control
• Direct editing
• Parent-child data inheritance
• Inspired by Natural History Guides
34. ViBRANT
Virtual Biodiversity
Scratchpad 2 “publication” options
Taxon descriptions
• Manuscripts from Scratchpads to ZooKeys & PhytoKeys
• Produced directly from the database
• Three exemplar papers produced via SP1
• Comprehensive new data structure in SP2
1. Define the 2. Enter 3. Select taxa 4. Organise 5. Submit to
publication metadata & content manuscript journal
