Community web sites: small pieces loosely joined

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Presented by Dave Roberts and coauthored by Simon Rycroft and Vince Smith at the GBIF European Nodes workshop at the National Muséum of Natural History (MNHN) in Paris, France. 4-6 April, 2011.

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Community web sites: small pieces loosely joined

  1. 1. ViBRANT Virtual Biodiversity Community web sites: small pieces loosely joined Dave Roberts, Simon Rycroft & Vince SmithSEVENTH FRAMEWORK PROGRAMME -infrastructure
  2. 2. ViBRANT Virtual BiodiversitySEVENTH FRAMEWORK PROGRAMME -infrastructure
  3. 3. ViBRANT Virtual Biodiversity Small pieces loosely joined Has many potential meanings: Joining contributors together to form communities Joining the data together that go towards forming a Scratchpad Joining Scratchpad content with the landscape of biodiversity informatics data on the webSEVENTH FRAMEWORK PROGRAMME -infrastructure
  4. 4. ViBRANT Virtual BiodiversityAddressing the challenges of 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 ... 4-6,000 taxonomists 30-40,000 “pro-amateurs” Many more citizen scientists?SEVENTH FRAMEWORK PROGRAMME -infrastructure
  5. 5. ViBRANT Virtual BiodiversityA website for you & your community Magic Your data Your web siteSEVENTH FRAMEWORK PROGRAMME -infrastructure
  6. 6. ViBRANT Virtual Biodiversity Dynamic web pages Taxonomy import, management and navigation Reference manager / Endnote support for bibliographies Image galleries, image upload & annotation Nexus / Newick import for visualising phylogenies Character matricies (discrete, morphometric and text characters) Presence / absence country maps Specimen & location records (DwC) Newsletters & Web fora with e-mail integration User blogsSEVENTH FRAMEWORK PROGRAMME -infrastructure
  7. 7. ViBRANT Virtual Biodiversity Import from CSV text file to any content typeSEVENTH FRAMEWORK PROGRAMME -infrastructure
  8. 8. ViBRANT Virtual Biodiversity Taxonomy & Literature Characters, Phylogeny & Specimens Lice, mosquitos, freeloader flies, ... Termites, bryozoa, ... (rapid upload and management of names, synonyms & bibliographic data) (character matrices exporting to SDD and Nexus format, phylogenies, specimen records & maps) 3000 Sites Registered Users 2500 240 Sites 200 2000 Users 160 1500 Taxon descriptions & Publications Image Galleries Freeloader Flies, fungus gnats, ... 120 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) 1000 80 500 40 0 0 Year 1 Year 2 Year 3 Year 4 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
  9. 9. ViBRANT Virtual BiodiversityViBRANT Products 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 compile taxonomic manuscripts automatically from their site. A portal for users to access public 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 biodiversity research community.SEVENTH FRAMEWORK PROGRAMME -infrastructure
  10. 10. ViBRANT Virtual Biodiversity Training Biodiversity & outreach data programme standards Networking User Controlled feedback vocabularyThe “chromosome” systems platform WP3. Training User sociology Data aggregation WP4. Standards study portal WP8. Mobilisation Field GBIF recording integration support activities Citizen Biodiversity science visualisation programme layers Scratchpads Virtual Research Service Research Environment Distributed Phylogenetic Scratchpad analysis hosting Bioclimatic Software WP5. Data modelling & metrics module integration WP2. Architecture WP6. Publishing WP7. Literature Identification Sustainability tools plan Communal Matrix data biodiversity editor literature Biodiversity Biodiversity data literature publishing markup Scholarly Biodiversity manuscript datamining publishingSEVENTH FRAMEWORK PROGRAMME -infrastructure
  11. 11. ViBRANT Virtual Biodiversity Training Biodiversity & outreach data programme standards GBIF Networking User Controlled feedback vocabularyThe “chromosome” systems GBIF platform WP3. Training User sociology Data aggregation WP4. Standards study portal WP8. Mobilisation Field GBIF recording integration support activities GBIF GBIF Citizen Biodiversity science visualisation programme layers GBIF Scratchpads Virtual Research Service Research Environment Distributed Phylogenetic Scratchpad analysis hosting Bioclimatic Software WP5. Data modelling & metrics module integration WP2. Architecture WP6. Publishing WP7. Literature Identification Sustainability tools plan Communal Matrix data biodiversity editor literature Biodiversity Biodiversity data literature publishing markup Scholarly Biodiversity manuscript datamining publishingSEVENTH FRAMEWORK PROGRAMME -infrastructure
  12. 12. ViBRANT Virtual Biodiversity “making the Scratchpads better” More reliable (e.g., distribute the servers) More functional (e.g., phylogenetic & publication services) Easier to use (better workflows) Prettier (better graphical design - more intuitive) More integrated (for data stored inside & outside the Scratchpad framework) More sustainable (simple administration, distribute developers, development sandbox) “making natural history better” Easier to compile, manage and reuse your data Easier to find and reuse other peoples data Promoting your data inside & outside the taxonomic community Getting people to work for you (crowdsourcing)SEVENTH FRAMEWORK PROGRAMME -infrastructure
  13. 13. ViBRANT Virtual Biodiversity Author Manuscript Public Enhanced preparation on HTML a Scratchpad PDF Submit as XML Enhanced XML Printed paper Produce PDF Send to Register with reviewers ZooBank, Publisher GBIF, EoL etc.SEVENTH FRAMEWORK PROGRAMME -infrastructure
  14. 14. ViBRANT Virtual Biodiversity https://git.scratchpads.eu/viewgitSEVENTH FRAMEWORK PROGRAMME -infrastructure
  15. 15. ViBRANT Virtual Biodiversity Thank you for your attention. Any questions e-mail: enquiries@vbrant.eu http://vbrant.eu http://scratchpads.euSEVENTH FRAMEWORK PROGRAMME -infrastructure

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