GLOBAL BIODIVERSITY

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/p
  roducts/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 worlds 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 GBIFs 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
GBIFs Participantscountries

• Currently has 78 Participants
• 47 countrieslatest Cameroon, Equatorial Guinea,
  Guinea, Philippines
• 26 Voting Participants 21 Associate Participants

14
GBIF membershiporganisations

• 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
GBIFs 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
GBIFs 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 gt90 million data records, from 168
  data providers from gt 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 comesearching 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
Species Name
Specimen Metadata
Indices - Catalog of Life - GBIF/ECAT Nomenclato
rs - Zoo Record - IPNI NameBank Publication
links - New species
GeoreferenceHabitatCharacter setsImagesBehavio
rOther genes
Barcode Sequence
Trace files
Literature(link to content or citation)
Other Databases
PhylogeneticPopn GeneticsEcological
20
(No Transcript)
21
(No Transcript)
22
(No Transcript)
23
Data quality

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

24
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 arent in geographic region
  indicated
• Mistakes in changing lat./long. from
  degrees-minutes-seconds to decimal degrees

25
How do we achieve a seamless web of
e-biodiversity resources?
26
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

27
GBIF plays a critical role in e-biodiversity
GBIF
28
How to contact GBIF
Web site www.gbif.org Data portal
www.gbif.net GBIF Secretariat Universitetsp
arken 152100 CopenhagenDenmark E-mail
gbif_at_gbif.org Phone [phone] Fax 45
3532 1480 GBIF Secretariat headquarters,
supported by grant from Aage V. Jensens Fonde