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GLOBAL BIODIVERSITY

GLOBAL BIODIVERSITY. INFORMATION FACILITY. Barcoding, bioinformatics and taxonomic research infrastructure. DNA Barcoding in Southern Africa Cape Town 7 April 2006. WWW.GBIF.ORG. Global Taxonomy Initiative. Established by Convention on Biological Diversity in 2002 (COP6)

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GLOBAL BIODIVERSITY

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  1. GLOBALBIODIVERSITY INFORMATIONFACILITY Barcoding, bioinformatics and taxonomic research infrastructure DNA Barcoding in Southern Africa Cape Town 7 April 2006 WWW.GBIF.ORG

  2. Global Taxonomy Initiative • Established by Convention on Biological Diversity in 2002 (COP6) • Purpose is to remove or reduce the ”taxonomic impediment”

  3. The taxonomic impediment • Knowledge gaps in our taxonomic system • Shortage of trained taxonomists and curators • Impact of these deficiencies on our ability to conserve, use and share the benefits of biological diversity

  4. Operational objectives of GTI • Assess taxonomic needs and capacities • Build and maintain human resources, systems and infrastructure • Facilitate improved and effective infrastructure for access to taxonomic information • Include taxonomic objectives in CBD work programmes and cross-cutting issues

  5. What is an effective infrastructure for taxonomy? • Taxonomists • Training • Access to information • Literature • Primary data • Research tools • Bandwidth • Other computing resources • Links to other biological web-based resources (e-biology/e-biodiversity)

  6. E-biodiversity • Web-based resources for biodiversity science • Includes: • Web-based tools (e.g. Lucid, DELTA) • Centralised databases (e.g. GenBank) • distributed networks of databases (e.g. GBIF) • Eventual goal is to link these resources together to provide a seamless user experience

  7. Some existing e-biodiversity resources • DNA sequence databases (GenBank et al.) (www.ncbi.nlm.nih.gov/Genbank) • Protein Data Bank (www.rcsb.org/pdb) • BOLD (www.barcodinglife.org) • Catalogue of Life (spice.sp2000.org) • Zoological Record (http://scientific.thomson.com/products/zr) • GBIF (www.gbif.net) • Cyber Infrastructure for Phylogenetic Research (CIPRES) (www.phylo.org) • Long-Term Ecological Research (LTER) Network (www.lternet.edu)

  8. Some future e-biodiversity resources • Biodiversity Heritage Library (www.bhl.si.edu) • European Distributed Institute for Taxonomy (EDIT) • Global Earth Observing System of Systems (GEOSS) (earthobservations.org)

  9. GBIF: a distributed data network

  10. What is GBIF ? An independent international organisation designed to • Make the world’s biodiversity data freely and universally available via the Internet, and especially to • Share primary scientific biodiversity data for science, society and a sustainable future

  11. What do we mean by primary biodiversity data? • Label data on ~ 1.5 - 3.0 billion specimens in natural history collections, herbaria, botanical gardens, etc. • Associated notes, recordings, publications, etc. • Observational data (e.g. bird banding data) • These data have been amassed over ~ 300 years; most not digital • Big legacy data problem

  12. Who are GBIF’s members ? • GBIF is a network of Participants • Each Participant agrees to • Share biodiversity data • Set up a Participant node(s) to organise its data providers and access the data • GBIF also works closely with the relevant international conventions and organisations • Especially the Convention on Biological Diversity, FAO, International Conservation Union, etc.

  13. GBIF’s Participants—countries • Currently has 78 Participants • 47 countries—latest Cameroon, Equatorial Guinea, Guinea, Philippines 26 Voting Participants 21 Associate Participants

  14. GBIF membership—organisations • 32 international organisations • Including • International Commission on Zoological Nomenclature • UNEP • Ocean Biogeographic Information System • World Conservation Union (IUCN) • SAFRINET • International Centre for Insect Physiology and Ecology • CBOL • Convention on Biological Diversity also has ex officio seat on the Governing Board

  15. Everything GBIF does is in partnership with others Global Strategy for Plant Conservation IUCN/Species Information Service CBD/Global Taxonomy Initiative

  16. GBIF’s IPR principles • Open access • All IPR stays with data providers • Data providers can restrict access to sensitive information • e.g. geographic coordinates of endangered species • Requires users to acknowledge source(s) of data • Cannot assure validity of any specific data in GBIF • But are making available tools to allow providers to clean up data and users to determine fitness of use of the data for their particular purposes

  17. GBIF’s programme areas • Data access and database interoperability (DADI) • Digitisation of specimen and observational data (DIGIT) • Electronic catalogue of names of known organisms (ECAT) • NODES • Outreach and capacity building (OCB)

  18. GBIF Data Portal • Prototype data portal opened in February 2004 • Now serves >90 million data records, from 168 data providers from > 30 countries • About 30% observational data, rest from natural history and living collections • Can search by species name, country, specimen • Two mapping tools • Soon to come—searching by locality, searching on more than one species at a time, linking to a wide range of other data (e.g. BOLD)

  19. Barcode Section of GenBank Voucher Specimen Link to GBIF Specimen Metadata Species Name GeoreferenceHabitatCharacter setsImagesBehaviorOther genes Indices - Catalog of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI NameBank Publication links - New species Barcode Sequence Trace files Literature(link to content or citation) Other Databases PhylogeneticPop’n GeneticsEcological

  20. Data quality • Three papers on data quality and use are available at www.gbif.org

  21. Data cleaning tools • GBIF has worked with CRIA (Brazil) to produce a suite of tools to check outliers in data • Differences in spelling • Georeferences with 0º lat. or long. • Localities that aren’t in geographic region indicated • Mistakes in changing lat./long. from degrees-minutes-seconds to decimal degrees

  22. How do we achieve a seamless web of e-biodiversity resources?

  23. Requirements for interoperability of databases • Standards • Barcode data record standards • Darwin core • DiGIR • GUIDs (Globally unique identifiers) • GBIF is working with the e-biodiversity community to develop a GUID scheme for species, specimens and collections

  24. GBIF plays a critical role in e-biodiversity GBIF

  25. How to contact GBIF • Web site: www.gbif.org • Data portal: www.gbif.net • GBIF Secretariat • Universitetsparken 152100 CopenhagenDenmark • E-mail: gbif@gbif.org • Phone: +45 3532 1470 • Fax: +45 3532 1480 • GBIF Secretariat headquarters, supported by grant from Aage V. Jensens Fonde

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