Sharing, linking and publishing biodiversity data the ViBRANT way


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Presentation given by Dave Roberts at the pro-ibiosphere conference in Leiden on February 11, 2013

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Sharing, linking and publishing biodiversity data the ViBRANT way

  1. 1. Scratchpad virtualresearch 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. 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. 3. Our informatics grand challenge… “Link together evolutionary This requires data, information data… by developing & knowledge to be… analytical tools and proper documentation and then •  Digital use this framework to Not printed paper conduct comparative •  Openly accessible analyses, studies of evolutionary process and Not behind barriers biodiversity analyses” •  Linked-up Not in silos Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001
  4. 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. 5. ViBRANT Virtual BiodiversityA website for you & your community Magic Your data Your web siteSEVENTH FRAMEWORK PROGRAMME -infrastructure
  6. 6. ViBRANT Virtual BiodiversityWhat are Scratchpads? • Hosted websites for biodiversity data • Virtual research & publication platform • Completely open access & open source • Modular & flexibleSEVENTH FRAMEWORK PROGRAMME -infrastructure
  7. 7. ViBRANT Virtual BiodiversityWhat 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 creatorSEVENTH FRAMEWORK PROGRAMME -infrastructure
  8. 8. ViBRANT Virtual BiodiversityHow are Scratchpads funded? 2007 2011 2014 ViBRANT Virtual Biodiversity &SEVENTH FRAMEWORK PROGRAMME -infrastructure
  9. 9. ViBRANT Virtual Biodiversity Taxonomy & Literature Lice, mosquitos, freeloader flies, ... Scratchpads Characters, Phylogeny & Specimens Termites, bryozoa, ... (character matrices exporting to SDD and Nexus format, phylogenies, specimen records & maps) biodiversity online (rapid upload and management of names, synonyms & bibliographic data) 7000 6000 Sites 5000 Users 4000 400 300 Active Users 3000 200 2000 100 Taxon descriptions & Publications Image Galleries Freeloader Flies, fungus gnats, ... 1000 Dragon trees, nanno fossils, cockroaches, fungi, polychaetes, ... (rapid upload, annotation & display of images) (publication of Scratchpad data in the ZooKeys journal and export to Encyclopedia of Life) 50 500 20 Users 2007 2008 2009 2010 2011 2012 Sites ViBRANT Scratchpads 2 eJournals Societies, Organisations & Projects European Mosquito Bulletin, Phasmid Studies, ... ICZN, GBIF, Sampled Red List Index for Plants, Global Plants Initiative ... (submission, review & dissemination of articles) (space for data collection, services, discussion & organisation)SEVENTH FRAMEWORK PROGRAMME -infrastructure
  10. 10. ViBRANT Virtual Biodiversity Training Data ViBRANT Goals & outreach standards Support Controlled services vocabulary Vision Networking Connecting the people, data & science of Sociology Training Standards Data aggregation Mobilisation biodiversity GBIF Field recording integration Citizen Visualisation Position science Scratchpads Open & sustainable development of a Virtual Research Environment federated network of biodiversity Phylogeny tools Scratchpad hosting informatics infrastructures Bioclimatic Software inte- modelling gration Mission Identification Sustainability tools Facilitate the mobalisation, sharing, Matrix data editor Communal literature reuse and publication of biodiversity data Data Literature publishing Service Research mark up Data Architecture Publishing Literature Manuscript publishing Data miningSEVENTH FRAMEWORK PROGRAMME -infrastructure
  11. 11. ViBRANT Virtual Biodiversity Taxonomic Concept Nexus Schema XML Newick CSV/tab Excel fileEoL Transfer schema (SPM) XML SDD, Lucid, CSV, XLS, DwCA RDF Nexus Microsoft Word .DOC, TXTSEVENTH FRAMEWORK PROGRAMME -infrastructure
  12. 12. ViBRANT Virtual BiodiversityWhat can Scratchpads do?• 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 integrationSEVENTH FRAMEWORK PROGRAMME -infrastructure
  13. 13. ViBRANT Virtual Biodiversity http://www.comber.hcmr.grSEVENTH FRAMEWORK PROGRAMME -infrastructure
  14. 14. ViBRANT Virtual Biodiversity Oxford Batch Operations Engine FRAMEWORK PROGRAMME -infrastructure
  15. 15. ViBRANT Virtual Biodiversity BDJ The Biodiversity Data Journal Making small data big!SEVENTH FRAMEWORK PROGRAMME -infrastructure
  16. 16. ViBRANT Virtual Biodiversity ISSN 1314-2828 (online) ISSN 1314-2836 (print)1. Define the A peer-reviewed open-access journal publication Biodiversity Articles D ata Journal Launched to accelerate biodiversity data journal Bibliographies 2. Enter metadata Occurrence3. Select taxa Taxon & content 1t 2011 treatments Plazi 4. Organise Taxon manuscript Editor-in-Chief: VINCENT SMITH Natural History Museum, London, UK names5. Submit to journal I . P . N . I SEVENTH FRAMEWORK PROGRAMME -infrastructure
  17. 17. ViBRANT Virtual BiodiversityAcknowledgements • 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+ usersSEVENTH FRAMEWORK PROGRAMME -infrastructure
  18. 18. ViBRANT Virtual Biodiversity Thank you for your attention. Any questions e-mail: e-mail: http://scratchpads.euSEVENTH FRAMEWORK PROGRAMME -infrastructure