ViBRANT—Virtual Biodiversity Research and Access Network for Taxonomy


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Presented by Dave Roberts and coauthored by Vince Smith at BioIdentify 2010, the National Muséum of Natural History (MNHN), Paris, France. 20-22 Sept, 2010.

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ViBRANT—Virtual Biodiversity Research and Access Network for Taxonomy

  1. 1. Project overview Dave Roberts, Simon Rycroft & Vincent S. Smith Natural History Museum, UK
  2. 2. The problem The challenges of 21 st century taxonomy 14 <ul><li>Inventory the Earth’s species </li></ul><ul><li>Document their relationships </li></ul><ul><li>“ Publish” & apply these data </li></ul>Goal… <ul><li>1.8 M described spp. (10M names) </li></ul><ul><li>300M pages (over last 250 years) </li></ul><ul><li>1.5-3B specimens </li></ul>Data set… People… <ul><li>4-6,000 taxonomists </li></ul><ul><li>30-40,000 “pro-amateurs” </li></ul><ul><li>Many more citizen scientists? </li></ul>
  3. 3. Towards a solution The European Distributed Institute of Taxonomy <ul><li>A Network of Excellence (NoE) </li></ul><ul><li>29 leading European, North American, </li></ul><ul><li>& Russian natural history collections-based </li></ul><ul><li>institutions </li></ul><ul><li>Circa 12M €, funded under EU FP6 </li></ul><ul><li>March 2006 - February 2011 </li></ul>14 Products… <ul><li>Funding </li></ul><ul><li>Training & outreach </li></ul><ul><li>Websites </li></ul><ul><li>Integrated scientific activities </li></ul><ul><li>Inventories </li></ul><ul><li>Computer tools </li></ul>
  4. 4. ViBRANT Building on the computer tools of EDIT “ To set up the means, tools and infrastructure to produce a more rational and a more effective framework for European Biodiversity research” 14 Connecting people… ViBRANT connects people studying biodiversity regardless of their location. Each community website ( Scratchpad ) contains tools and services that enable users to study biodiversity in all its different facets. Connecting data… Information about biodiversity is scattered in a myriad of different places. ViBRANT helps defragment this information providing a window on the natural world that can be filtered according to users needs. Connecting science… ViBRANT bridges the gap between the producers & consumers of taxonomic information, providing the tools to help explain & predict the distribution of life on Earth.
  5. 5. ViBRANT Products <ul><li>A Virtual Research Environment ( Scratchpads ) where users can safely store, share and manage their research information. </li></ul><ul><li>Analytical services for users to build identification keys and phylogenetic trees. </li></ul><ul><li>A publication platform for users to automatically compile taxonomic manuscripts from their research database. </li></ul><ul><li>A portal for users to centrally access publicly accessible biodiversity research information and literature. </li></ul><ul><li>Training & support , helping research communities to use these tools and services. </li></ul><ul><li>A standards compliant technical architecture that can be sustained by biodiversity research community. </li></ul>The highlights 14
  6. 6. Users & logistics <ul><li>Starts December 2010 (36 months) </li></ul><ul><li>Project website ( ) </li></ul><ul><li>Virtual Research Communities, CP-CSA, EU FP7 </li></ul><ul><li>€ 6.2M Euros (EU Contribution €4.75M) </li></ul><ul><li>17 Partners in 9 countries, 603 person months </li></ul>User communities <ul><li>Anyone with an interest in biodiversity (research to citizen scientists) </li></ul><ul><li>Supporting taxonomic regional and thematic communities </li></ul><ul><li>Facilitate eBooks, eJournals, Conservation assessments, flora & faunal studies, data collection, community vocabularies, citizen science projects </li></ul><ul><li>Success measured through user engagement </li></ul>Logistics 14
  7. 7. ViBRANT Partners <ul><li>The Natural History Museum, London (NHM) </li></ul><ul><li>- Scratchpad VRE development & management </li></ul><ul><li>Hellenic Center for Marine Research, Crete (HCMR) </li></ul><ul><li>- Extension into ecol.,con. & citizen science, esp. marine biodiversity </li></ul><ul><li>Royal Belgian Institute of Natural Sciences (RBINS) </li></ul><ul><li>- Training, outreach & community support </li></ul><ul><li>Oxford e-Research Centre (UOXF.E9) </li></ul><ul><li>- Mol. ID tools, services and data analysis </li></ul><ul><li>Vrije Universiteit Amsterdam (VU) </li></ul><ul><li>- User studies (sociological studies of user practices) </li></ul><ul><li>Julius Kühn-Institute (JKI) </li></ul><ul><li>- Data integration via controlled vocabularies & ontologies </li></ul><ul><li>Museum für Naturkunde, Berlin (MFN) </li></ul><ul><li>- Biodiversity inventorying & monitoring (mobile devices) </li></ul><ul><li>University of Amsterdam (UvA) </li></ul><ul><li>- Standards development (PESI) </li></ul><ul><li>The Open University (OU) </li></ul><ul><li>- Data mining and bibliographies (BHL) </li></ul><ul><li>Karlsruher Institut für Technologie (KIT) </li></ul><ul><li>- Document Markup & natural language text processing </li></ul><ul><li>Vizzuality (Vizz) </li></ul><ul><li>- Data visualisation & analysis (data layers) </li></ul><ul><li>Pensoft Publishers (PENSOFT) </li></ul><ul><li>- Push-button manuscript submission from the Scratchpad VRE </li></ul><ul><li>Université Pierre et Marie Curie-Paris 6 (UPMC) </li></ul><ul><li>- Morphological identification keys and services (Xper 2 ) </li></ul><ul><li>Global Biodiversity Information Facility (GBIF) </li></ul><ul><li>- Controlled vocab. dev. & userbase expansion via GBIF nodes </li></ul><ul><li>Freie Universität Berlin (BGBM) </li></ul><ul><li>- Data aggregation portal via CDM </li></ul><ul><li>Université de la R é union (UdlR) </li></ul><ul><li>- Mathematics & HCI of taxonomic identification keys </li></ul><ul><li>University of Trieste </li></ul><ul><li>- Key2Nature integration & outreach </li></ul>17 partners in 9 countries (universities, museums, research centres, SMEs) 14
  8. 8. International aspects <ul><li>LifeWatch - prototype service centre ( ) </li></ul><ul><li>ELIXIR - taxonomic metadata services ( ) </li></ul><ul><li>EMBRC - supporting marine model organism research ( ) </li></ul>ESFRI collaboration… Global collaboration… <ul><li>GBIF - controlled vocabularies, nodes & observational data recording </li></ul><ul><li>PESI, 4D4Life & related EU projects </li></ul><ul><li>Encyclopedia of Life, Barcode of Life & Biodiversity Heritage Library </li></ul><ul><li>South African National Biodiversity Institute & Atlas of living Australia </li></ul>14
  9. 9. Project plan The “chromosome” 14 SERVICE WP5. Data WP6. Publishing WP4. Standards WP8. Mobalisation RESEARCH WP2. Architecture WP7. Literature NETWORKING WP3. Training
  10. 10. Scratchpads Community focal point Scratchpads Virtual Research Environment 160+ research communities 14 N S R
  11. 11. Scratchpads Overview <ul><li>Hosted websites for taxonomists </li></ul><ul><li>Research & publication platform </li></ul><ul><li>Modular (Drupal) & flexible </li></ul><ul><li>Supports the taxonomic workflow </li></ul><ul><li>Bottom-up design, agile dev. </li></ul><ul><li>Ecosystem of communities (150+) </li></ul><ul><li>2,000+ users (unpaid) from 2007 </li></ul>14 N S R
  12. 12. Scratchpads ViBRANT’s hub 14 N S R <ul><li>Taxonomic, regional & thematic communities </li></ul><ul><li>Electronic books </li></ul><ul><li>Electronic journals </li></ul><ul><li>Conservation priorities </li></ul><ul><li>Biodiversity assessment </li></ul><ul><li>Citizen science </li></ul><ul><li>Controlled data </li></ul>
  13. 13. Become involved <ul><li>Start a Scratchpad for your community ( ) </li></ul><ul><li>Register to join an existing Scratchpad community ( ) </li></ul><ul><li>Attend a training course, or apply for one to come to your community ( ) </li></ul><ul><li>Access data - COMING SOON ( ) </li></ul><ul><li>Become a part of the software development team ( & ) </li></ul><ul><li>20-21 January 2011, Grande Galerie de I’Evolution, Muséum national d’histoire naturelle </li></ul><ul><li>Further details to follow ( ) </li></ul>Opening conference… 14
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