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Building Sustainable Biodiversity Information Systems

Building Sustainable Biodiversity Information Systems. Fredrik Ronquist Dept. Bioinformatics and Genetics Swedish Museum of Natural History. Who am I?. Lead the development of MorphBank, an open web repository for biodiversity images, 1998–2007

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Building Sustainable Biodiversity Information Systems

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  1. Building Sustainable Biodiversity Information Systems Fredrik Ronquist Dept. Bioinformatics and Genetics Swedish Museum of Natural History

  2. Who am I? • Lead the development of MorphBank, an open web repository for biodiversity images, 1998–2007 • Organizing the DINA-Specify effort, an international initiative to develop an open-source web-based system for collection management • Our group is a partner or node in GBIF, LifeWatch, EU-BON / GEO BON, BalticDiversity • We contribute or have contributed to BioCASE, OpenUp, PESI, Synthesys, etc • Since 2011 a member of the Swedish Research Council panel on eScience infrastructure

  3. A Global Network of Regional Centers? European Center for Biodiversity Information North American Center for Biodiversity Information Asian Center for Biodiversity Information African Center for Biodiversity Information South American Center for Biodiversity Information Australian Center for Biodiversity Information

  4. Involves 29 mostly European partners • Aims to build a substantial part of the Group on Earth Observation’s Biodiversity Observation Network (GEO BON) • Will provide ”near-real-time data — both from on-ground observations and remote sensing — to stake holders and end users ranging from local to global levels” • ”... intends to develop a full-scale model for a durable mechanism for higher level integration of biodiversity information providers and users through a network of networks approach scalable from local to global biodiversity observation systems” • Advance technological/informatics infrastructures for GEO BON • Improve the range and quality of methods and tools for assessment, analysis, and visualization of drivers of change and biodiversity indicators • Five-year project 2012–2017. Long-term sustainability: LifeWatch (?)

  5. A European infrastructure in development • Part of the ESFRI Roadmap 2006 (ESFRI = European Strategy Forum on Research Infrastructures) • Preparatory phase 2008–2011 with participation of 19 European countries • Currently five participating countries (Hungary, Italy, The Netherlands, Romania, Spain) • Major national LifeWatch initiatives include Swedish LifeWatch, ~ 5 M € budget for 2010-2014, coordinated by the Swedish Species Information Centre in Uppsala • Focus in Swedish LifeWatch is on development of analytical tools for Swedish biodiversity and climate data • Long-term sustainability? • For analytical and visualization tools, not for digitization or for systems for digital asset management and data delivery? • Will the project gin traction in Europe? • LifeWatch – GBIF competing for funds?

  6. The Collaborative Approach • Collaboration means significant social and technical challenges • Success requires modular design of large systems to allow semi-independent development in contributing development teams • Some parallel development is unavoidable and even desirable • Coordinating efforts and maintaining a consistent overall system is challenging • Establishment of standard interfaces to modules: a role for TDWG • Natural History Collection Institutions provide a good institutional platform for sustainable solutions: • Long-term time perspective • Digital assets - just another collection • Strong community increasingly used to international collaborations • eScience competence improving rapidly • Long-term perspective requires patience

  7. DINA(Digital Information System for Natural History Data) • Web-based system for assembling, managing and sharing data associated with natural history collections • Scope includes botany, zoology, paleontology, geology, observation records, molecular data and living collections • Based on cross-institutional open-source development starting with Specify and Morphbank as initial building blocks • Aim is national or large-institution installations servicing multiple institutions and a range of users, from professional collection managers and curators to collections-oriented citizen scientists • Current consortium partners include software development teams as well as institutions or national initiatives interested in hosting software installations • Project info and news at http://dina-project.net

  8. DINA-Specify Consortium • Current partners • Biodiversity Institute (Specify team), University of Kansas, USA • Botany and Biodiversity Informatics, Agriculture and Agri-Food Canada, Ottawa, Canada • Museum für Naturkunde, Berlin, Germany • Natural History Museum, University of Tartu, Estonia • Danish Museum of Natural History, Copenhagen, Denmark • Swedish Museum of Natural History, Stockholm, Sweden • Royal Botanic Garden, Edinburgh • Possibly Harvard University Herbaria, Harvard University, USA • Memorandum of Cooperation ready for signing before the end of the year (download from http://dina-project.net)

  9. Consortium Structure • Core members: • Commit a full-time equivalent of staff resources to the development of consortium goals, including at least a half-time resource for software development • Are represented in the SETF and are expected to contribute actively to its work • Commit to work under SETF guidelines • Associate members: • Commit to support consortium goals • Do not commit any staff resources and are not represented in the SETF • Provide technical expertise and feedback on system design • Funding of consortium contributions may involve both temporary and permanent funding sources • Members may change their status (associate or core) at any time with previous notice and due respect to previous commitments to the consortium • Members may leave the consortium at any time • Memorandum of Cooperation has a five-year time frame with possibility of extension

  10. DINA: EU-BON Objectives • Integrate DINA-Specify with taxonomic backbone for Europe and other tools (e.g. molecular biodiversity data and digitization tools) developed within EU-BON • Improve data mobilization through real-time sharing of data across relevant networks (GBIF, BioCASEetc) • Development of citizen science (amateur naturalists) interface to the system • Development of interfaces in relevant EU-BON languages • Support for EU-BON institutions that would like to install the system • Support for institutional and citizen-science users of the system • Participate in targeted digitization and mobilization efforts based on gap analysis

  11. Consortium Organization International Steering Committee (all members) Task Force I System Engineering Task Force (core members) Task Force II Development Team 1 Development Team II Development Team III

  12. DINA organization Agriculture Canada, Ottawa, Canada Sweden NRM Specify team Kansas, USA NRM Steering Group Digital Collection Managers Natural History Museum, Tartu Museum für Naturkunde, Berlin DINA-SE development team DINA-DK DINA-SE steering group DINA International Council

  13. DINA-SE development team Karin Karlsson (50 %) Kevin Holston Markus Skyttner Ida Li Markus Englund (80 %) Ingimar Erlingsson

  14. Modularization of DINA-Specify

  15. Acknowledgements • DINA-Specify consortium partners • Swedish Museum of Natural History • EU BON • BalticDiversity (EU Regional Development Fund) • Swedish GBIF node • Swedish LifeWatch • Swedish Research Council

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