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Roberts leiden110213

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  • 1. Scratchpad virtual research environments: sharing, linking and publishing biodiversity data the ViBRANT way Vince Smith1, Dave Roberts1 & Lyubomir Penev2 1. Natural History Museum, London 2. Pensoft Publishers, Sofia, Bulgaria
  • 2. Our informatics grand challenge… “Link together evolutionary data… by developing analytical tools and proper documentation and then use this framework to conduct comparative analyses, studies of evolutionary process and biodiversity analyses” Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001
  • 3. Our informatics grand challenge… “Link together evolutionary data… by developing analytical tools and proper documentation and then use this framework to conduct comparative analyses, studies of evolutionary process and biodiversity analyses” Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001 This requires data, information & knowledge to be… •  Digital Not printed paper •  Openly accessible Not behind barriers •  Linked-up Not in silos
  • 4. Most of our output is not digital, open or linked •  •  •  •  •  •  15-20k new spp. described annually (2M total)1 30k nomenclatural acts (12M total) 1 20k phylogenies (750k total)2 31k taxa sequenced (360k taxa total)3 800k BioMed papers (40M total pp. of taxonomy) 4 Countless specimens, images, maps, keys… Typically generated by small communities for “local” research projects Figures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.
  • 5. ViBRANT Virtual Biodiversity A website for you & your community Magic Your data SEVENTH FRAMEWORK PROGRAMME Your web site -infrastructure
  • 6. ViBRANT Virtual Biodiversity What are Scratchpads? • Hosted websites for biodiversity data • Virtual research & publication platform • Completely open access & open source • Modular & flexible SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 7. ViBRANT Virtual Biodiversity What Scratchpads are not! • A single biodiversity database • Restricted thematically, geographically or taxonomically • A tool just for taxonomists • Owned or controlled by anyone other than the data creator SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 8. ViBRANT Virtual Biodiversity How are Scratchpads funded? 2007 2011 2014 ViBRANT Virtual Biodiversity & SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 9. ViBRANT Virtual Biodiversity Scratchpads Taxonomy & Literature Lice, mosquitos, freeloader flies, ... (rapid upload and management of names, synonyms & bibliographic data) Characters, Phylogeny & Specimens Termites, bryozoa, ... (character matrices exporting to SDD and Nexus format, phylogenies, specimen records & maps) biodiversity online 7000 6000 5000 4000 Sites Users Active Users 400 300 3000 200 2000 100 Taxon descriptions & Publications 1000 50 Sites 20 eJournals European Mosquito Bulletin, Phasmid Studies, ... (submission, review & dissemination of articles) SEVENTH FRAMEWORK PROGRAMME Dragon trees, nanno fossils, cockroaches, fungi, polychaetes, ... (rapid upload, annotation & display of images) 500 2007 2008 2009 2010 2011 2012 ViBRANT Scratchpads 2 Users Freeloader Flies, fungus gnats, ... (publication of Scratchpad data in the ZooKeys journal and export to Encyclopedia of Life) Image Galleries Societies, Organisations & Projects ICZN, GBIF, Sampled Red List Index for Plants, Global Plants Initiative ... (space for data collection, services, discussion & organisation) -infrastructure
  • 10. ViBRANT Virtual Biodiversity Training & outreach Support services ViBRANT Goals Vision Connecting the people, data & science of biodiversity http://vbrant.eu SEVENTH FRAMEWORK PROGRAMME Controlled vocabulary Networking Training Standards Mobilisation Sociology Data aggregation Field recording GBIF integration Citizen science Position Open & sustainable development of a federated network of biodiversity informatics infrastructures Mission Facilitate the mobalisation, sharing, reuse and publication of biodiversity data Data standards Visualisation Scratchpads Virtual Research Environment Scratchpad Phylogeny tools hosting Bioclimatic modelling Software integration Identification tools Matrix data editor Data publishing Service Data Publishing Manuscript publishing Sustainability Communal literature Research Literature mark up Architecture Literature Data mining -infrastructure
  • 11. ViBRANT Virtual Biodiversity Taxonomic Concept Schema XML Nexus Newick CSV/tab Excel file EoL Transfer schema (SPM) SDD, Lucid, DwCA Nexus SEVENTH FRAMEWORK PROGRAMME XML CSV, XLS, RDF Microsoft Word .DOC, TXT -infrastructure
  • 12. ViBRANT What can Scratchpads do? Virtual Biodiversity • Taxon pages (generated from tagged content) • Distribution maps (from specimens and TDWG regional distributions - Brummitt, 2001) • Specimen records • Bibliography management • Images, video and sound (bulk import) • Excel spreadsheet import • Tabular data editing & Character matrixes • Custom content • User management • Custom webforms • Analytics • Darwin Core Archive export (links to eMonocot Portal and EOL) • EOL data import (taxonomy, species information) • GBIF Map integration SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 13. ViBRANT Virtual Biodiversity http://www.comber.hcmr.gr SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 14. ViBRANT Virtual Biodiversity Oxford Batch Operations Engine https://oboe.oerc.ox.ac.uk/ SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 15. ViBRANT Virtual Biodiversity BDJ The Biodiversity Data Journal Making small data big! SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 16. ViBRANT Virtual Biodiversity ISSN 1314-2828 (online) ISSN 1314-2836 (print) 1. Define the publication A peer-reviewed open-access journal Biodiversity D ata Journal Articles Launched to accelerate biodiversity data journal Bibliographies 2. Enter metadata Occurrence 3. Select taxa & content 1t 2011 Taxon treatments Plazi http://www.pensoft.net/biodiversitydata 4. Organise manuscript Editor-in-Chief: VINCENT SMITH Natural History Museum, London, UK Taxon names 5. Submit to journal I . P . N . I SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 17. ViBRANT Virtual Biodiversity Acknowledgements • Scratchpad technical development - Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine Boulton • Scratchpad outreach - Laurence Livermore & Dimitris Koureas • E-Monocot - Paul Wilkin & the Kew team, Charles Godfray & the Oxford team • ViBRANT - Vince Smith, Dave Roberts & Lucy Reeve • Our 7,000+ users SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 18. ViBRANT Virtual Biodiversity Thank you for your attention. Any questions e-mail: enquiries@vbrant.eu e-mail: scratchpad@nhm.ac.uk http://vbrant.eu SEVENTH FRAMEWORK PROGRAMME http://scratchpads.eu -infrastructure