ViBRANT 8th e-Concertation Meeting, CERN


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A short overview of the ViBRNAT project presented by Vince Smith at the 8th eConcertation meeting in CERN, Geneva on 5th November, 2010.

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  • Good morning everybody. My name is Vincent Smith; I am a research scientist based at the Natural History Museum in London and am the coordinator the ViBRANT consortium. ViBRANT stands for Virtual Biodiversity Research and Access Network for Taxonomy, and despite the rather long title, the name is a good reflection of what we are trying to do. ViBRANT is about the creation of a virtual infrastructure that supports the mobilisation, sharing, reuse and publication of biodiversity data. Our goal is to link up many the major European biodiversity initiatives, to provide an integrated framework for that supports the the monitoring and management of information about ecosystems and natural resources. As part of the Virtual Research Communities call our strategy is bottom-up, user driven, and builds on the success of products built in prior EU funded the projects.
  • Partners
    To achieve this we have put together a consortium of 17 partners in 9 countries representing many of the leading players in European biodiversity informatics. Our partners include universities, museums, research centres, and 2 industrial enterprises. This team includes software developers, IT infrastructure specialists, research scientists, sociologists and experts in professional training. Each was chosen because of their proven experience in the field of biodiversity informatics. [The consortium has a wide geographic spread, stretching from the University of Oxford in the West, to Sofia, Bulgaria and the Hellenic Centre for Marine research in the East. We also stretch as far South as the Reunion Island off the coast of Madagascar - a French overseas territory in the Indian Ocean.]
    Our primary audience are biodiversity scientists. In particular we are seeking to engage members of the taxonomic and systematic research communities that work on describing and documenting flora and fauna. It’s estimated that this is a relatively small community of perhaps no more than 10,000 scientists worldwide. Fortunately there is a large community of so-called professional amateurs who we engage with. [These are people not necessarily affiliated with professional associations but work to professional standards. It is estimated that there are upwards of 40,000 people that meet this definition worldwide.] And finally though some targeted projects we are engaging citizen scientists who can spare some of their time participating in virtual projects to support particular research and data gathering activities.
    At the moment our user base for the core infrastructure that is supported through ViBRANT is about 2,400. These scientists and amateurs are spread across 192 different research communities. Each of these have very varied special interests, although most are either taxonomic or geographically defined communities interested in particular flora and fauna. At a lower level there is a much wider network of people engaging in the products of ViBRANT’s partners, and one of the goals of ViBRANT is to more effectively integrate these products so that users can more easily benefit form these activities.
    ESFRI collaboration
    ViBRANT is integrated with the three ongoing ESFRI projects that are relevant to biodiversity research. The first is LIFEWATCH: ViBRANT will act as the prototype service centre for the LIFEWATCH project. The second is ELIXIR – the European Bioinformatics Institutes infrastructure project. ViBRANT will be providing taxonomic metadata services to ELIXIR to enhance accessibility of their data. Finally ViBRANT will provide its community research infrastructure to EMBRC – the network of European Marine research laboratories that are working on marine model organisms.
    Wider collaboration
    We also are engaged with a number of other large EU and global projects. Of particular note are GBIF the Global Biodiversity Information Facility. GBIF is in fact a partner in the project. We are working with several EU projects including PESI, the Pan European Species Infrastructure. We also have data links to the Encyclopedia of Life Initiative, the Consortium for the Barcode of Life, and the Biodiversity Heritage Library, each of which are major global biodiversity initiatives. We also have small project links with SANBI in South Africa and the Atlas of Living Australia.
  • At its core, ViBRANT’s mission statement is “to set up the means, tools and infrastructure to produce a more rational and a more effective framework for European Biodiversity research”. Fundamentally this means linking up the people, the data and the science of biodiversity, through a common and interoperable infrastructure.
    We are doing this by building an infrastructur that is key to providing this connectivity.
    This consists of:
    キA Virtual Research Environment (something we call Scratchpads) where users can safely store, share and manage their data.
    キAnalytical services for users to build identification keys and phylogenetic trees.
    キA publication platform for users to automatically compile manuscripts from their research database.
    キA portal for users to centrally access publicly accessible biodiversity research information and literature.
    キTraining, support & sociological study, helping research communities to use these tools and services.
    キA standards compliant technical architecture that can be sustained in the long term by biodiversity research community.
    The kinds of products our users have already generated from this infrastructure are listed at the bottom of this slide. These include things like electronic Books and electronic Journals; conservation assessments; flora and faunal studies; long term data monitoring repositories; community vocabularies to help standardise the way we describe biodiversity; identification guides and citizen science projects.
    That concludes my presentation. You can find more information on the ViBRANT website or by e-mailing us. Thanks for your time.
  • ViBRANT 8th e-Concertation Meeting, CERN

    1. 1. Virtual Biodiversity ViBRANT 8th e-Infrastructure Concertation Meeting CERN, Geneva, November 4-5th 2010 Vincent S. Smith Natural History Museum, UK ViBRANT Virtual Biodiversity
    2. 2. 2 of Virtual Biodiversity ViBRANT Who we are 3 • 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 • University of Trieste - Key2Nature integration & outreach 17 partners, 9 countries • LifeWatch - prototype service centre • ELIXIR - taxonomic metadata services • EMBRC - marine model organism research ESFRI collaboration… Wider collaboration… • GBIF - thesauri, nodes & data recording • PESI, 4D4Life & related EU projects • EOL, CBoL & BHL • SANBI & Atlas of living Australia • 2,392 core users • 192 biodiversity communities • Tens of thousands through partner networks Current users • Biodiversity scientists • Professional “amateurs” • Citizen scientists Audience
    3. 3. 3 of Virtual Biodiversity ViBRANT What we do 3 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. • 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. E-Infrastructure products Example community products • eBooks, eJournals, conservation assessments, flora and faunal studies, long term data monitoring repositories, communitie vocabulariers, identification guides, citizen science projects. More at Or