TDWG_ ViBRANT_301013

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TDWG (Firenze 2013) Description of the ViBRANT project. 30th Oct 2013

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TDWG_ ViBRANT_301013

  1. 1. ViBRANT Virtual Biodiversity ViBRANT: progress towards an integrated framework Vince Smith & Dave Roberts SEVENTH FRAMEWORK PROGRAMME -infrastructure
  2. 2. ViBRANT Virtual Biodiversity ViBRANTs contribution 17 partners in 9 countries (universities, museums & SMEs) Interoperability, workflows, services, information modeling & user support SEVENTH FRAMEWORK PROGRAMME -infrastructure
  3. 3. 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
  4. 4. ViBRANT Virtual Biodiversity ViBRANT Outputs E-Infrastructure • • • • • • 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 to centrally access publicly accessible 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. Products (extra-network activities because of the infrastructure) • • • Content: eBooks, eJournals, Con. assessments, flora and faunal studies, long term data repositories, community vocabulariers, id. guides, citizen science projects. Code: Drupal modules, OBOE services New sectors of interest: agriculture, education SEVENTH FRAMEWORK PROGRAMME -infrastructure
  5. 5. ViBRANT Virtual Biodiversity Knowledge Organization System GBIF Service migrated to GBIF Secretariat (hosting) TDWD VoMaG task group installed (governance) Species-ID Semantic Media Wiki Integrated with GBIF-KOS system Scratchpad Common Access point CDM <–> Scratchpad and CDM <–> Xper2 pipelines Pipelines further defined via DwC-A extensions & SDD Improved data interfaces & API New vocabularies supported (e.g. Audubon Core) Development of APIs on the CDM Liaise with major initiatives TDWG, EOL, EU-BON, & LifeWatch SEVENTH FRAMEWORK PROGRAMME -infrastructure
  6. 6. ViBRANT Virtual Biodiversity 200 180 160 Users 140 120 100 80 60 40 20 0 2011 2012 2013 1000 900 800 Tasks 700 600 500 400 300 200 100 Oxford Batch Operations Engine SEVENTH FRAMEWORK PROGRAMME 0 https://oboe.oerc.ox.ac.uk/ -infrastructure
  7. 7. ViBRANT Virtual Biodiversity http://biblife.org RefBank nodes http://zoobank.org/RefBank more nodes coming soon .... Currently holds about 210,000 references Citations growing at about 5,000 / month SEVENTH FRAMEWORK PROGRAMME -infrastructure
  8. 8. ViBRANT Virtual Biodiversity Number of Citations Papers mentioning a Scratchpad Site 90 80 70 60 10000 8000 50 40 10 0 2008 2009 2010 Number of Citations 2011 600 2012 400 300 Papers mentioning the Scratchpad Project Sites 25 20 6000 5000 4000 Sites Users Active Users 20 3000 2000 200 1000 100 15 10 50 5 30 0 2008 SEVENTH FRAMEWORK PROGRAMME 2009 2010 2011 2012 Users 30 500 2007 2008 2009 2010 ViBRANT 2011 2012 2013 Scratchpads 2 -infrastructure
  9. 9. ViBRANT Virtual Biodiversity irtual http://www.comber.hcmr.gr SEVENTH FRAMEWORK PROGRAMME -infrastructure
  10. 10. ViBRANT The target audience: Nodes that have limited web presence. Virtual Biodiversity The approach: Using the country checklist generated from the GBIF mediated data to dynamically retrieve biodiversity information from GBIF & EOL. The result: A web portal that is easy to set up, customise, and enables joint development. An example site at http://nptstartup.gbif.org The code is available at https://git.scratchpads.eu/git/scratchpads-2.0.git as a branch “gbif-npt-startup” Import the checklist requested separately by writing to nodes@gbif.org http://links.gbif.org/npt Finish the setup with initial news and textual contents SEVENTH FRAMEWORK PROGRAMME -infrastructure
  11. 11. ViBRANT Virtual Biodiversity PWT or Scratchpads About Pensoft Books E-Books Journals News & Blog Register | Login Contact Start a manuscript All Author Title How it works Articles About Journal features 1. Define the publication Resolving the publishing bottleneck for biodiversity Focus and Scope Globally unique innovations Criteria for publication Peer review For authors Data publication Science is a combination of gathering facts and making theories; neither can progress on its own. In the history of science, the laborious accumulation of facts is the dominant mode, not a novelty. Publication fees Licenses and Copyright Frequently Asked Questions (FAQ) Contacts Editorial team Most visited papers This work is licensed under the Creative Commons Attribution 3.0 (CC-BY). Making “small” data big No lower/upper limit of manuscript size Publish all kinds of biodiversity related data Reduced page charges affordable by all More than just data journal! Integrated text and data publishing Completely online revisions and editing Community ownership of data Community peer-review 3 days from acceptance to publication Public peer-review on author’s choice Why publish my data? Increase collaboration Re-use and multiply effect Taxon treatments Plazi Establish scientific priority Link data to a bigger network 4. Organise manuscript Citable publication Occurrence 7 weeks from submission to decision Free of charge in launch phase 3. Select taxa & content Bibliographies Peter Norvig Follow us 2. Enter metadata Articles Respond to funding requirements Editor-in-Chief: VINCENT SMITH Natural History Museum, London, UK Taxon names 5. Submit to journal I . P . N . I SEVENTH FRAMEWORK PROGRAMME -infrastructure
  12. 12. ViBRANT Virtual Biodiversity Be agile Users need Lessons Have a Champion Deliver an immediate benefit to users Market your products!!! SEVENTH FRAMEWORK PROGRAMME -infrastructure

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