Global Biodiversity Information Facility GLOBAL BIODIVERSITY INFORMATION FACILITY DNA Barcoding in Southern Africa Cape Town 7 April Barcoding, bioinformatics and taxonomic research infrastructure

Global Biodiversity Information Facility Global Taxonomy Initiative l Established by Convention on Biological Diversity in 2002 (COP6) l Purpose is to remove or reduce the ”taxonomic impediment”

Global Biodiversity Information Facility The taxonomic impediment l Knowledge gaps in our taxonomic system l Shortage of trained taxonomists and curators l Impact of these deficiencies on our ability to conserve, use and share the benefits of biological diversity

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

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

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

Global Biodiversity Information Facility Some existing e-biodiversity resources l DNA sequence databases (GenBank et al.) ( l Protein Data Bank ( l BOLD ( l Catalogue of Life (spice.sp2000.org) l Zoological Record ( l GBIF ( l Cyber Infrastructure for Phylogenetic Research (CIPRES) ( l Long-Term Ecological Research (LTER) Network (

Global Biodiversity Information Facility Some future e-biodiversity resources l Biodiversity Heritage Library ( l European Distributed Institute for Taxonomy (EDIT) l Global Earth Observing System of Systems (GEOSS) (earthobservations.org)

Global Biodiversity Information Facility GBIF: a distributed data network

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

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

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

Global Biodiversity Information Facility GBIF’s Participants—countries l Currently has 78 Participants l 47 countries—latest Cameroon, Equatorial Guinea, Guinea, Philippines 26 Voting Participants21 Associate Participants

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

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

Global Biodiversity Information Facility GBIF’s IPR principles l Open access l All IPR stays with data providers l Data providers can restrict access to sensitive information l e.g. geographic coordinates of endangered species l Requires users to acknowledge source(s) of data l Cannot assure validity of any specific data in GBIF l 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

Global Biodiversity Information Facility GBIF’s programme areas l Data access and database interoperability (DADI) l Digitisation of specimen and observational data (DIGIT) l Electronic catalogue of names of known organisms (ECAT) l NODES l Outreach and capacity building (OCB)

Global Biodiversity Information Facility GBIF Data Portal l Prototype data portal opened in February 2004 l Now serves >90 million data records, from 168 data providers from > 30 countries l About 30% observational data, rest from natural history and living collections l Can search by species name, country, specimen l Two mapping tools l 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)

Barcode Sequence Voucher Specimen Link to GBIF Species Name Specimen Metadata Literature (link to content or citation) Barcode Section of GenBank Indices - Catalog of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI NameBank Publication links - New species Georeference Habitat Character sets Images Behavior Other genes Trace files Other Databases Phylogenetic Pop’n Genetics Ecological

Global Biodiversity Information Facility

Data quality l Three papers on data quality and use are available at

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

Global Biodiversity Information Facility How do we achieve a seamless web of e-biodiversity resources?

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

Global Biodiversity Information Facility GBIF plays a critical role in e-biodiversity GBIF

Global Biodiversity Information Facility How to contact GBIF Web site: Data portal: GBIF Secretariat Universitetsparken Copenhagen Denmark Phone: Fax: GBIF Secretariat headquarters, supported by grant from Aage V. Jensens Fonde