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ViBRANT Project Overview

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Presented at Scripting Life: the science behind ViBRANT, at the Grande Galerie de l'Evolution, Paris, France on 20th and 21st January 2011.

Presented at Scripting Life: the science behind ViBRANT, at the Grande Galerie de l'Evolution, Paris, France on 20th and 21st January 2011.

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  • 1. ViBRANT Virtual Biodiversity ViBRANT Virtual BiodiversityVirtual Biodiversity Research and Access Network for Taxonomy: Project Overview Vince Smith Natural History Museum, London vince@vsmith.info
  • 2. ViBRANT Virtual BiodiversityOutline • Some background / why ViBRANT? • Goals / what makes ViBRANT different • What ViBRANT will do • Logistics & collaboration • Measures of success • Longer term vision ViBRANT Virtual Biodiversity 2 of 27
  • 3. ViBRANT Virtual BiodiversityOutline • Some background / why ViBRANT? • Goals / what makes ViBRANT different • What ViBRANT will do • Logistics & collaboration • Measures of success • Longer term vision ViBRANT Virtual Biodiversity 3 of 27
  • 4. ViBRANT Virtual BiodiversityOur problemThe challenge of 21st Century taxonomy 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… • 4-8,000 taxonomists • 30-40,000 “pro-amateurs” • Many more citizen scientists? 4 of 27
  • 5. ViBRANT Virtual BiodiversityA solutionThe transformative role of the internet & the World Wide Web You are here • Built of links The 1st Internet • 1 trillion pages 4-node ARPAnet - 1969 • 2 billion users from Hobbes’ Internet timeline (http://bit.ly/dtBJ2i) 5 of 27
  • 6. ViBRANT Virtual BiodiversityThe web applied to taxonomyBiodiversity informatics TDWG Projects Database 663 projects (Jan. 2011) 6 of 27
  • 7. ViBRANT Virtual BiodiversityTowards a solutionThe 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 7 of 27
  • 8. ViBRANT Virtual BiodiversityScratchpadshttp://scratchpads.eu • Hosted websites for taxonomists • Research & publication platform • Modular (Drupal) & flexible • Supports the taxonomic workflow • 2,500 users (unpaid) from 2007 • Ecosystem of communities (~200) 8 of 27
  • 9. ViBRANT Virtual Biodiversity9 of 27
  • 10. ViBRANT Virtual BiodiversityOutline • Some background / why ViBRANT? • Goals / what makes ViBRANT different • What ViBRANT will do • Logistics & collaboration • Measures of success • Longer term vision ViBRANT Virtual Biodiversity 10 of 27
  • 11. ViBRANT Virtual Biodiversity11 of 27
  • 12. ViBRANT Virtual BiodiversityGoals of ViBRANT To set up the means, tools and infrastructure to produce a more rational and a more effective framework for European Biodiversity research.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. 12 of 27
  • 13. ViBRANT Virtual BiodiversityWhat we will doE-Infrastructure products • A Virtual Research Environment (Scratchpads) where users can safely store, share and manage data. • Analytical services for users to build identification keys and phylogenetic trees. • A publication platform for users to automatically compile manuscripts from their research database. • A portal for users the best Virtual Research Environment Creating to centrally access publicly accessible biodiversity research information and literature. & systematic research community for the taxonomic • Training, support & sociological study, helping research communities to use these tools and services. • A standards compliant technical architecture that can be sustained by biodiversity research community. ViBRANT is primarily a tool, secondarily a data provider 13 of 27
  • 14. ViBRANT Virtual BiodiversityWho is doing it • The Natural History Museum, London (NHM) - Scratchpad VRE development & management • Hellenic Center for Marine Research, Crete (HCMR) - Extension into ecol.,con. & citizen science, esp. marine biodiversity • Royal Belgian Institute of Natural Sciences (RBINS) - Training, outreach & community support • Oxford e-Research Centre (UOXF.E9) - Mol. ID tools, services and data analysis • Vrije Universiteit Amsterdam (VU) - User studies (sociological studies of user practices) • Julius Kühn-Institute (JKI) - Data integration via controlled vocabularies & ontologies • Museum für Naturkunde, Berlin (MFN) - Biodiversity inventorying & monitoring (mobile devices) • University of Amsterdam (UvA) - Standards development (PESI) • The Open University (OU) - Data mining and bibliographies (BHL) • Karlsruher Institut für Technologie (KIT) - Document Markup & natural language text processing • Vizzuality (Vizz) - Data visualisation & analysis (data layers) • Pensoft Publishers (PENSOFT) - Push-button manuscript submission from the Scratchpad VRE • Université Pierre et Marie Curie-Paris 6 (UPMC) - Morphological identification keys and services (Xper2) • Global Biodiversity Information Facility (GBIF) - Controlled vocab. dev. & userbase expansion via GBIF nodes • Freie Universität Berlin (BGBM) - Data aggregation portal via CDM • Université de la Réunion (UdlR) - Mathematics & HCI of taxonomic identification keys 17 partners in 9 countries • University of Trieste (universities, museums & SMEs) - Key2Nature integration & outreach 14 of 27
  • 15. ViBRANT Virtual BiodiversityWhat makes ViBRANT different Its (mostly) not research ViBRANT is primarily about tools & services Its is about audiences ViBRANT is driven by its users (old & new) Our work program is flexible Re-writing our deliverables is one of the deliverables! ViBRANT is agile The perpetual beta - like taxonomy ViBRANT is sustainable We do things simply & cheaply, such that we can maintain them 15 of 27
  • 16. ViBRANT Virtual BiodiversityOutline • Some background / why ViBRANT • Goals / what makes ViBRANT different • What ViBRANT will do • Logistics & collaboration • Measures of success • Longer term vision ViBRANT Virtual Biodiversity 16 of 27
  • 17. 8 of 14 ViBRANT Virtual BiodiversityMacro Organisation (CP-CSA) • WP1. (435,125 €) Management, coordination & administration (7 partners) Networking Activities (1,805,885 €) • WP3. (683,242 €) Training, outreach & community support (4) • WP4. (713,784 €) Standardisation (5) • WP8. (408,859 €) Ecological and conservation data mobilization (5) Service Activities (1,025,578 €) • WP5. (755,913 €) Interaction and data services (5) • WP6. (269,665 €) Scholarly Publishing (2) Research Activities (1,483,411 €) • WP2. (858,495 €) Technical architecture (2) • WP7. (624,916 €) Biodiversity literature data access & data mining (4) 17 of 27
  • 18. ViBRANT Virtual BiodiversityViBRANT Project planThe “chromosome” NETWORKING WP4. Standards WP3. Training WP8. Mobilisation SERVICE RESEARCH WP5. Data WP2. Architecture WP6. Publishing WP7. Literature 18 of 27
  • 19. ViBRANT Virtual BiodiversityOutline • Some background / why ViBRANT • Goals / what makes ViBRANT different • What ViBRANT will do • Logistics & collaboration • Measures of success • Longer term vision ViBRANT Virtual Biodiversity 19 of 27
  • 20. ViBRANT Virtual BiodiversityViBRANT logistics • Started 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 monthsCollaboration (not just EU)… • 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 20 of 27
  • 21. ViBRANT Virtual BiodiversityOutline • Some background / why ViBRANT • Goals / what makes ViBRANT different • What ViBRANT will do • Logistics & collaboration • Measures of success • Longer term vision ViBRANT Virtual Biodiversity 21 of 27
  • 22. ViBRANT Virtual BiodiversityShort term success metricsUser engagement as a measure of success*Networking (tools and collaboration) • How many people are using our tools • How deep is their engagement with these tools • How are these tools changing what they would otherwise doServices (data & processing data) • How much internal data is being called from outside the system • How much external data is being called from inside the system • How much are our services being used to add valueResearch (discovery of new information or approaches) • Traditional academic metrics (publications, presentations, blogs etc) • Uptake within ViBRANT & outside the consortium both quantitative & qualitative (WP3)* 22 of 27
  • 23. ViBRANT Virtual BiodiversityLonger term success metricsOnce ViBRANT project is overPersistence & sustainability • Maintaining what we do (perhaps without money) • If its valued, it will endure • Not everything will persist!Finding new audiences • ViBRANT is primarily about taxonomy & taxonomists • Engage more people as “taxonomists” (e.g. citizen scientists) • Reach out to other sectors e.g. conservation & ecologyEmbed our products outside the consortium • Take up by other initiatives, especially outside the EU • E.g. LifeWatch service centre, GBIF Nodes, publishers, CBoL, EoL 23 of 27
  • 24. ViBRANT Virtual BiodiversityOutline • Some background / why ViBRANT • Goals / what makes ViBRANT different • What ViBRANT will do • Logistics & collaboration • Measures of success • Longer term vision ViBRANT Virtual Biodiversity 24 of 27
  • 25. ViBRANT Virtual Biodiversity(My) Longer term visionTaxonomy’s three problems, & my view of how we fix them Defragmenting our output • Tools that support technical & social workflows of taxonomy • Provide the means to (loosely) aggregate that content ViBRANT Virtual Biodiversity Speeding up out output • Digitising collections • Increasing our workforce (engaging non-professionals) • Coordinated & standardised programs for new kinds of output Improved labeling & findability • Simple & persistent identifiers on defined concepts of everything • Simplifying how we define (publish) concepts 25 of 27
  • 26. ViBRANT Virtual BiodiversityWhere taxonomy is nowAnd where we might like to be… You are here • Built of links The 1st Internet • 1 trillion pages 4-node ARPAnet - 1969 • 2 billion users from Hobbes’ Internet timeline (http://bit.ly/dtBJ2i) 26 of 27
  • 27. ViBRANT Virtual Biodiversity27 of 27