GLOBAL BIODIVERSITY

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GLOBALBIODIVERSITY
INFORMATIONFACILITY
The Global Biodiversity Information Facility An
Interoperable Network of Primary Biodiversity
Databases Jim Edwards, Campinas, Brazil, 4 March
2004
WWW.GBIF.ORG
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What is GBIF ?

• A network of Participant nodes that
• Make primary biodiversity data openly and freely
  available over the Internet
• Use common standards for data and metadata
• Encourage generation of additional content
• Assure that data providers retain control of
  their own data
• Provide access to biodiversity data through a
  single portal

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Why was GBIF established?

• Georeferenced biodiversity data of good quality
  and historical depth resides in the worlds
  natural history collections and observational
  databases
• These data were being digitised in a haphazard,
  piecemeal fashion
• GBIF was formed to help synergise and pull
  together species- and specimen-level databases
  and make them interoperable

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Why was GBIF established?

• Both biodiversity and biodiversity data are
  unevenly distributed around the world

• GBIF is helping to redress the inequality of data
  distribution

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GBIF ...

• Was recommended by an OECD working group and
  endorsed by OECD science ministers
• But is independent from the OECD
• Is not part of the United Nations
• But works closely with many UN bodies
• Convention on Biological Diversity
• World Conservation Monitoring Centre
• Is based on a non-binding Memorandum of
  Understanding between countries and international
  organisations

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Each Participant in GBIF agrees to

• Share scientific biodiversity data
• Develop an Internet node to access those data
• In addition, Voting Participants agree to
• Make a specific contribution toward GBIFs
  activities

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GBIF Voting Participants 25

• Netherlands
• New Zealand
• Nicaragua
• Norway (Feb. 2004)
• Portugal
• Peru
• Slovenia
• South Africa
• Spain
• Sweden
• UK
• USA

• Australia
• Belgium
• Canada
• Costa Rica
• Denmark
• Estonia
• Finland
• France
• Germany
• Iceland
• Japan
• Republic of Korea
• Mexico

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GBIF Associate Participants 16 24

• ALL Species Foundation
• ASEANET
• BioNET
• BIOSIS
• CABI Bioscience
• EASIANET
• European Commission
• Expert Centre for Taxonomic Identification
• Freshwater Biological Association
• Inter-American Biodiversity Information Network
• Integrated Taxonomic Information System
• IUCN
• NatureServe
• Ocean Biogeographic Information System
• SAFRINET
• Société de Bactériologie Systématique et
  Vétérinaire
• Species 2000
• Taxonomic Databases Working Group
• UNESCO Man and the Biosphere Program

• Argentina
• Austria
• Bulgaria
• Colombia
• Czech Republic
• Ghana
• India
• Madagascar
• Morocco
• Pakistan
• Papua/New Guinea (Feb 04)
• Poland
• Slovak Republic
• Switzerland
• Taiwan
• Tanzania

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GBIFs focus is on primary data

• Primary data result from the direct observation
  of nature, for example
• A specimen of an organism
• Banding a bird

• Primary data can be used and reused to answer
  many kinds of questions, both scientific and
  societal

• Georeferenced primary data can be analysed in
  many ways, e.g.
• Choosing best sites for conservation areas or
  future biodiversity collecting efforts
• Predicting effects of climate change on biota
• Choosing best sites for GMO field trials
• Predicting the spread of invasive species

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What are GBIFs primary data ?

• Label data on 1.5 - 3.0 billion specimens in
  natural history collections

• Associated notes, recordings, observational
  databases, etc.
• These data must be digitised in order to be
  shared and fully utilised

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Example The Cactus Moth Cactoblastis cactorum

• Study done by Jorge Soberon, CONABIO, Mexico, and
  collaborators
• Cactoblastis devours every single species of
  prickly-pear (Platyopuntia) cactus that has been
  examined
• In the US and Mexico there are more than 90
  species of Platyopuntia, many endangered, that
  are vital components of arid ecosystems.
• In Mexico, Platyopuntia is the 10th most
  important agricultural product

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Cactoblastis cactorum
Data points obtained from the NMNH, USA
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Climate surface obtained by Floramap (12 layers)
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Platyopuntia localities MNHSD, IBUNAM, ENCB,
MOBOT, NMNH, UAH
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Predicted number of species of Platyopuntia
Opuntia lagunae Fotografías de la planta y el
fruto de Jon Rebman Fotografía de las flores de
George Lindsay http//www.oceanoasis.org/fieldgui
de/opun-lag-sp.html
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Vulnerable areas to Cactoblastis (right climate
and right food)
Red isolines High similarity to climate in the
original Cactoblastis cactorum sites.
Blue regions Richness of species of
Platyopuntia.
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What does GBIF do ?

• GBIF has a set of tasks that is distinct from
  that of any other organization.
• In order to promote the sharing and use of
  scientific biodiversity data by everyone, it
  focuses on four areas of activity
• Digitisation of Natural History Collections
  (DIGIT)
• Electronic Catalog of Names of Known Organisms
  (ECAT)
• Data Access and Database Interoperability (DADI)
• Outreach and Capacity Building (OCB)

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GBIF contribution to interoperability
Until now, it has not been possible to combine
data from GenBank with specimen and ecological
data from other sources without painstaking work
by a person.
With GBIFs components in place, data can be
drawn directly from different sources with a
single query.
Compiled specimen, genetic, and ecological
information
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Prototype of GBIF data portal now open for use
and comment

• www.gbif.net
• Currently contains gt12 million specimen and
  observational records,
• Provided by more than 34 data record providers
  and about 20 names providers
• Can search on scientific names (including
  synonyms), see record information, plot maps, get
  lists of taxa by country, etc.
• Portal still in prototype stage
• Expect to add many more records and to improve
  search methodologies throughout 2004
• Please provide comments to help us improve it!!

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GBIFs contributions to interoperability

• Work with Taxonomic Databases Working Group
  (TDWG) to establish standards for data and
  interoperability
• E.g., Darwin Core, DiGIR, GIS standards
• Work with Catalogue of Life and others to finish
  Electronic Catalogue of the worlds scientific
  names by 2010
• Including consensus taxonomy, synonyms, common
  names
• Will be an authority file for use by all

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GBIFs support for biodiversity informatics

• Database components of several activities of the
  Convention on Biological Diversity
• Clearing House Mechanism, Global Taxonomy
  Initiative, Global Strategy for Plant
  Conservation
• Seed-money grants for digitisation and for
  developing components of the Electronic Catalogue
• GBIF-UNESCO Chairs in Biodiversity Informatics
• Begin 2005 with 4 chairs in developing countries,
  2 in developed
• White papers on IPR, digitisation technologies,
  etc.
• Training courses
• Ebbe Nielsen Prize

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Contact details
Jim Edwards jedwards_at_gbif.org www.gbif.org GBIF
Secretariat Universitetsparken 15 Copenhagen
2100 DENMARK New GBIF Secretariat
headquarters, supported by grant from Aage V.
Jensens Fonde
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GBIF Voting Participants 25

• Netherlands
• New Zealand
• Nicaragua
• Norway
• Portugal
• Peru
• Slovenia
• South Africa
• Spain
• Sweden
• UK
• USA

• Australia
• Belgium
• Canada
• Costa Rica
• Denmark
• Estonia
• Finland
• France
• Germany
• Iceland
• Japan
• Republic of Korea
• Mexico

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GBIF Associate Participants 15 24

• ALL Species Foundation
• ASEANET
• BioNET
• BIOSIS
• CABI Bioscience
• EASIANET
• European Commission
• Expert Centre for Taxonomic Identification
• Freshwater Biological Association
• Inter-American Biodiversity Information Network
• Integrated Taxonomic Information System
• IUCN
• NatureServe
• Ocean Biogeographic Information System
• SAFRINET
• Société de Bactériologie Systématique et
  Vétérinaire
• Species 2000
• Taxonomic Databases Working Group
• UNESCO Man and the Biosphere Program

• Argentina
• Austria
• Bulgaria
• Colombia
• Czech Republic
• Ghana
• India
• Madagascar
• Morocco
• Pakistan
• Poland
• Slovak Republic
• Switzerland
• Taiwan
• Tanzania

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What is GBIF ?

• GBIF is a megascience facility aimed at
• Making the worlds biodiversity data freely and
  universally available via the Internet
• Sharing primary scientific biodiversity data for
  society, science and a sustainable future

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What is GBIF?

• A distributed facility, comprising an ever-
  growing network of Participant nodes that
• Share biodiversity data openly and freely
• Use common standards for data and metadata
• Encourage generation of additional content
• Assure that data providers retain control of data

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Why was GBIF established ?

• Both biodiversity and biodiversity data are
  unevenly distributed around the world

• GBIF was established, in large part, to redress
  the inequality of data distribution

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Why was GBIF established ?

• To undertake biodiversity informatics activities
  that must be accomplished on a worldwide basis in
  order to make the Internet into a highly
  valuable, dynamic library of biological
  information
• To take on tasks not being attempted by other
  initiatives but which would be of benefit to
  those initiatives (e.g. CHM, GTI, others)
• To make biodiversity databases interoperable
  among themselves and with molecular, genetic,
  ecological and other types of databases, thus
  increasing the value of all of them

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True bioinformatics
bioinformatics
ecoinformatics
genomics
proteomics
biodiversity informatics
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GBIF contribution to interoperability
Until now, it has not been possible to combine
data from GenBank with specimen and ecological
data from other sources without painstaking work
by a person.
With GBIFs components in place, data can be
drawn directly from different sources with a
single query.
Compiled specimen, genetic, and ecological
information
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Data Interoperability...
Observational Dataset
6 records
35 records
Museum A
17 records

• 81 records
• Museum A Paris
• Museum A Nice
• Museum A Paris
• Museum A Avignon
• Museum A Avignon
• Museum A Marseille
• Observer X Norwich
• Observer X Norwich
• Observer X Southampton
• . . .

Museum B
GBIF
Culture collection
0 records
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GBIF deals with 1 biodiversity data
o
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GBIF works cooperatively

• Recently signed Memo of Cooperation with the
  Catalogue of Life partnership
• Also work with the Taxonomic Databases Working
  Group of CODATA on data standards

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Users and applications need data structured
according to standards
lt?xml version"1.0" encoding"UTF-8"?gt ltresponsegt
ltrecordgt ltdarwinDateLastModifiedgt2003-06-08lt/d
arwinDateLastModifiedgt ltdarwinInstitutionCodegt
DGHlt/darwinInstitutionCodegt ltdarwinCollectionC
odegtDGH Lepidopteralt/darwinCollectionCodegt ltdar
winCatalogNumbergtDGHEUR_0002976lt/darwinCatalogNu
mbergt ltdarwinScientificNamegtDichomeris
marginella (Fabricius, 1781)lt/darwinScientificNam
egt ltdarwinBasisOfRecordgtOlt/darwinBasisOfRecord
gt ltdarwinKingdomgtAnimalialt/darwinKingdomgt ltd
arwinOrdergtLepidopteralt/darwinOrdergt ltdarwinF
amilygtGelechiidaelt/darwinFamilygt ltdarwinGenusgt
Dichomerislt/darwinGenusgt ltdarwinSpeciesgtmargin
ellalt/darwinSpeciesgt ltdarwinScientificNameAuth
orgt(Fabricius, 1781)lt/darwinScientificNameAuthorgt
ltdarwinIdentifiedBygtDonald Hobernlt/darwinIden
tifiedBygt ltdarwinCollectorgtDonald
Hobernlt/darwinCollectorgt ltdarwinYearCollectedgt
2003lt/darwinYearCollectedgt ltdarwinMonthCollect
edgt06lt/darwinMonthCollectedgt ltdarwinDayCollect
edgt08lt/darwinDayCollectedgt ltdarwinContinentOce
angtEuropelt/darwinContinentOceangt ltdarwinCountr
ygtDenmarklt/darwinCountrygt ltdarwinCountygtGentof
te Amtlt/darwinCountygt ltdarwinLocalitygtMerianve
j, Helleruplt/darwinLocalitygt ltdarwinLongitudegt
12.538lt/darwinLongitudegt ltdarwinLatitudegt55.73
7lt/darwinLatitudegt ltdarwinCoordinatePrecisiongt
100lt/darwinCoordinatePrecisiongt ltdarwinIndivid
ualCountgt1lt/darwinIndividualCountgt ltdarwinNote
sgt1 in Skinner traplt/darwinNotesgt lt/recordgt lt/re
sponsegt
Observation record formatted using the Darwin Core
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GBIF Information Architecture
User Requests
GBIF Data Nodes
Biodiversity Data Access Portal
Biodiversity Data Index
Catalogue of Life
Taxo-nomic Name Service (ECAT)
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Web services enable the aggregation of structured
data
Web Services
Data indexing registry are part of these
Heterogeneous Databases
Standardised Structured Data
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But it isnt an easy task...
which is why GBIF is a megascience activity...
and why training in biodiversity informatics is
needed
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