GLOBAL
BIODIVERSITY
INFORMATION
FACILITY
Beatriz Torres
Seminar on GBIF - Norway
25 September 2003
WWW.GBIF.ORG
Global Biodiversity Information Facility
Present challenges around the world for
Natural History Collections
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Legislators and university administrators often see museums/herbaria
as “exhibit halls”.
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How to address?: Planned and current cutbacks in museums and
science collections are quite dramatic in many parts of the world
(i.e. USA from 10-30% of budget cutbacks to whole collections being
closed down).
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Decreased funding from research councils for collections.
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To preserve collections, scientists need to do a better job of
explaining the role of natural history collections in serving science
and society.
Global Biodiversity Information Facility
Emerging new field: biodiversity informatics
•
Biodiversity informatics is the
application of information technology
to biology with the emphasis on
persistent biodiversity data stores.
R. Robbins, Fred Hutchinson Cancer Research Center
Global Biodiversity Information Facility
DNA
Biodiversity
Informatics
Proteins
Phenotypes
Populations
Species
Abiotic Factors
Ecosystems
Global Biodiversity Information Facility
Adapted from R. Robbins
Bioinformatics
Persistent
Primary
Data
Stores
Map
Databases
DNA
PDB
Proteins
GenBank
EMBL
DDBJ
SwissPROT
PIR
Phenotypes
Populations
Species
Abiotic Factors
Ecosystems
Global Biodiversity Information Facility
Adapted from R. Robbins
GBIF Mission
Megascience project aimed at
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Making the world’s biodiversity data freely
and universally available via the Internet
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Sharing primary scientific biodiversity data
to benefit science and society.
Global Biodiversity Information Facility
Why was GBIF established ?

To undertake biodiversity informatics activities that
must be accomplished on a worldwide basis
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To take on tasks not being attempted by other
initiatives but which would be of benefit to those
initiatives
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
To ensure that scientists around the world can benefit
from accessing and using biodiversity data
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Global Biodiversity Information Facility
How was it established ?
l
OECD Sub-Group of the Megascience Forum
Working Group on Biological Informatics (96-99)
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Recommendations were endorsed by the OECD
Ministers (June 1999).
An interim steering committee for GBIF was
established to negotiate GBIF’s Memorandum of
Understanding (1999-2000).
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Global Biodiversity Information Facility
When was GBIF started ?

GBIF came into existence on 1 March 2001, when the
first 10 countries signed the Memorandum of
Understanding (MoU) and pledged a total of US$2M
Global Biodiversity Information Facility
What is GBIF ?
A distributed facility, comprising a
network of Participant NODES that
Share biodiversity data openly and freely
 Use common data and metadata standards
 Encourage generation of additional content
 Data providers retain control and ownership
of their data
 Gain access to others’ data by sharing theirs
(credit to sources)
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Global Biodiversity Information Facility
GBIF Participants
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Voting Participants are countries that
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Sign the Memorandum of Understanding (MoU)
Establish and maintain a GBIF node
Contribute financially to GBIF’s Work Programme
Associate Participants are countries,
economies or international organisations
that
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Sign the Memorandum of Understanding
Establish and maintain a GBIF node
Global Biodiversity Information Facility
GBIF Voting Participants
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Australia
Belgium
Canada
Costa Rica
Denmark
Estonia
Finland
France
Germany
Iceland
Japan
Republic of Korea
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24
Mexico
Netherlands
New Zealand
Nicaragua
Portugal
Peru
Slovenia
South Africa
Spain
Sweden
UK
USA
Global Biodiversity Information Facility
GBIF Associate Participants 15 + 20
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ALL Species Foundation
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ASEANET
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BioNET
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BIOSIS
Colombia
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CABI Bioscience
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Czech Republic
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EASIANET
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Ghana
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Expert Centre for Taxonomic Identification (ETI)
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Madagascar
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Inter-American Biodiversity Information Network (IABIN)
Morocco
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Integrated Taxonomic Information System (ITIS)
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IUCN – The World Conservation Union.
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Pakistan
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NatureServe
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Poland
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Ocean Biogeographic Information System (OBIS)
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Slovak Republic
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SAFRINET
Switzerland
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Société de Bactériologie Systématique et Vétérinaire
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Species 2000
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Taiwan
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Taxonomic Databases Working Group (TDWG)
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Tanzania
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UNESCO Man and the Biosphere Program
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European Commission
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UNEP (World Conservation Monitoring Centre)
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World Federation for Culture Collections (WFCC)
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Wildscreen Trust
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Argentina
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Austria
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Bulgaria
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Global Biodiversity Information Facility
Benefits of GBIF - data providers
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Higher visibility of the institution or
research project as useful to society
Global dissemination of the data
 Source of the data attributed when used
 Build strong cases to access more funding
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Contribution to the ability of everyone
to share in the common store of
humanity’s knowledge about biodiversity
Global Biodiversity Information Facility
Benefits of GBIF - biodiversity researchers
GBIF as a distributed megascience facility will provide
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access to a persistent data store for specimen- and specieslevel data, thus filling a niche similar to that of GenBank for
DNA-level data
easy online access to geo-referenced specimen data via a
network portal
a complete, global, index to scientific names and thus to the
scientific literature electronic and databases
a means to link together data from disparate sources (e.g.
DNA, specimen, species observation and ecosystem) to
answer complex questions
opportunities for within- and cross-disciplinary collaboration
a means to infuse biodiversity policy and management
decisions with real, scientific data
Global Biodiversity Information Facility
More benefits of GBIF’s network
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Both biodiversity and biodiversity data are
unevenly distributed around the world:
Developed World
Developing World
Biodiversity
Data
Biodiversity
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GBIF assist scientists in developing countries to have access to data
on specimens housed all over the world (CBD. art. 17).
Global Biodiversity Information Facility
Benefits of GBIF - developing countries
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Access to data and information associated with a
country’s specimens that are housed in foreign
institutions
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Travel to obtain the data not required
Difficulty of repatriating and expense of housing actual
specimens is avoided
Ability to share fully in the common store of
humanity’s knowledge about biodiversity
Opportunity for training in the expert development
and use of biodiversity information
GBIF support of and in cooperation with others i.e.
the CBD (CHM, GTI, 2010 halting biodiversity loss
initiative) will help to build in-country capacity and
expertise.
Global Biodiversity Information Facility
GBIF Vision for Uses of Biodiversity Data
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Sustainable
Industry
Conser- Regu- Development
vation lation
General
Edu- Public
cation
Research
…..
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…..
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Primary data
Reuse of data,
avoidance of
duplication of
effort
Primary data
available for
different users
Interoperability
with other kinds
of data (genetic,
molecular,
geographic, etc.)
Alleviation of gaps
in knowledge
Global Biodiversity Information Facility
Characteristics of Biodiversity Data
Biological entities are more complex than all
other physical and chemical entities:
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At all levels of organization, each biological entity is
unique
Phylogenetic (genealogical) history matters a great deal
Biological relationships are intricate, and contingent
upon, and therefore complicated by
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Ecology (including symbioses & parasitic relationships)
Behavior
Chemical competencies
Sensibility, vagility, mobility, etc.
Global Biodiversity Information Facility
GBIF’s area of data responsibility
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The types of data
that GBIF will
facilitate are
unique; while
encouraging no
duplication of
efforts.
The return on the
investments made
in the other areas
will be enhanced
by the data and
interoperability
provided by GBIF.
Global Biodiversity Information Facility
GBIF contribution to interoperability
Compiled specimen, genetic, and
ecological information
Example: 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 GBIF’s
components in place,
data can be drawn
directly from different
sources with a
single query.
Global Biodiversity Information Facility
What does GBIF do ?
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In order to promote the sharing and use of
scientific biodiversity data GBIF focuses on
four areas of activity:
 Digitisation of Natural History Collections (DIGIT)
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Electronic Catalog of Names of Known Organisms
(ECAT)
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Data Access and Database Interoperability (DADI)
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Outreach and Capacity Building (OCB)
Global Biodiversity Information Facility
Digitisation of Natural History Collections (DIGIT)
To facilitate the expansion of
biodiversity knowledge by
having legacy and newly
acquired primary species
occurrence data digitised and
dynamically accessible.
Global Biodiversity Information Facility
What are GBIF’s primary data ?
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Label data on ~ 1.5 - 3.0 billion specimens in
natural history collections
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Associated notes,
recordings, observational
databases, etc.
These data must be
digitised in order to be
shared and fully utilised
Global Biodiversity Information Facility
Data Access and Database Interoperability (DADI)
To facilitate the full use of
biodiversity and other
databases by establishing an
information architecture that
enables interoperability and
facilitates data-mining
Global Biodiversity Information Facility
How can GBIF data be made to
interoperate with other data ?
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By devising
and
adopting
common
data and
metadata
standards
and
software
protocols
ECAT elements
have been
coloured orange:
GBIF Portal
XML Data Access
HTML Data Access
“Name Lists” are
lists of names for
a specific purpose
(e.g. Red List,
Biodiversity Data Access
GBIF Data
Nodes
regional checklist)
Specimen
Data
Observation
Data
Name Lists
Index
Manager
Indexing
of usage
Indexing
of usage
Name Usage
Index
Taxonomic
Name
Service
(ECAT)
Catalogue of
Life
Unstructured
Data URLs
Global Biodiversity Information Facility
How can GBIF data be made to interoperate?
Example: Find Global Specimens/Observations
Retrieve specimen/observation records (e.g. for a given species or
location) held by any part of the GBIF Network
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By carefully
thinking
through the
individual
logical and
logistical steps
needed to
accomplish the
larger goal
6 records
Show records of Erinaceus
europaeus
35 records
17 records
81 records:
1.
2.
3.
4.
5.
6.
7.
8.
9.
Museum A
Museum A
Museum A
Museum A
Avignon
Museum A
Avignon
Museum A
Marseille
Observer X
Norwich
Observer X
Norwich
Observer X
Southampton
Paris
Nice
Paris
GBIF
23 records
...
Global Biodiversity Information Facility
How can GBIF data be made to
interoperate with other data ?
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By developing a complete,
electronic listing of all
the names of all the
species that are known to
science, which also
accommodates various
classifications
Argiope bruennichi (Scopoli) 1796
Global Biodiversity Information Facility
Electronic Catalog of Names of Known Organisms (ECAT)
To facilitate the exploration
and rapid expansion of
biodiversity knowledge by
providing a complete, digital
listing of the names of all
known organisms
Global Biodiversity Information Facility
Why are names so important ?
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The scientific name is the only
data field common to all these
different databases
Specimen
Data
GenBank,
etc.
Search
Engine(s)
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Tree of Life
Without a scientific name, there
is no access to primary data
Ecological
Databases
Global Biodiversity Information Facility
Why are names so important ?
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Where does this invasive
species come from?
Specimen
Data
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What do we know about
its genes?
GenBank,
etc.
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What is it related to?
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What are its ecological requirements?
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What are its predators?
Tree of Life
Ecological
Databases
Specimen
Data
+
GIS layers
Global Biodiversity Information Facility
How can GBIF benefits be shared by all ?
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Establish capacity to take
advantage of the data
that GBIF facilitates and
makes available
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Train people
Build infrastructure
Protect intellectual
property rights (ownership
remains with data
providers)
Global Biodiversity Information Facility
Outreach and Capacity
Building (OCB)
Through training and capacity
building, ensure that scientists,
NODE managers and decisionmakers in every country have
access to and can use the world’s
biodiversity data and information
Global Biodiversity Information Facility
GBIF Summary
Sharing of biodiversity data via the web
 Data providers retain control over it.
 Protection of intellectual property rights
 Distributed network architecture
 Common standards and protocols
 Partnership with other networks
 Avoidance of duplication of effort
 Promotion of technical developments to
deal with complexity of biodiversity data
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Global Biodiversity Information Facility
GBIF works in cooperation with others
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In cooperation with and in support of
organisations that need biodiversity
information, such as the Convention on
Biological Diversity:
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Clearing House Mechanism (CHM)
Global Taxonomy Initiative (GTI)
In partnership with such other initiatives as
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Species 2000 and the Integrated Taxonomic
Information Service (ITIS)—the “Catalog of Life”
Taxonomic Database Working Group (TDWG)
Global Biodiversity Information Facility
GBIF Organizational Chart
Governing Board
Secretariat
Executive Committee
Standing Committees
Ad hoc Committee
Membership
Science
Budget
NODES
ECAT
OCB
Science Subommittees
DADI
DIGIT
Global Biodiversity Information Facility
GBIF Governance
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Governing Board (GB) meets twice a year
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Establishes policy
Oversees finances through its Budget Committee
Delegates actions between meetings to Executive
Committee
Secretariat
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Carries out GBIF Work Programme
Coordinates activities of the nodes
Promotes GBIF principles
Encourages participation in GBIF
Recommends policies to Governing Board
Global Biodiversity Information Facility
How does GBIF work ?
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NODES Committee
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Comprises the managers of the Participant nodes
Works with the Information and Communications
Technology (ICT) staff of the Secretariat to develop
the network of nodes
Participant nodes share software and ideas
with each other and with data providers
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Secretariat ICT staff advise, coordinate and provide
software toolkits
Global Biodiversity Information Facility
How to join GBIF
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GBIF Memorandum of Understanding (MoU)
WWW.GBIF.ORG
Send letter of intent to Chair of the Governing
Board
Sign and send MoU and establish GBIF node
Arrange payment of annual contribution (for
Voting Participation)
If an individual or institution, participate in
GBIF through your country’s node or a node of
one of the Associate Participants
Global Biodiversity Information Facility
GBIF Schedule of Contributions
GDP in
billions of US $
Annual GBIF
contribution
> 3000
700,000
2000 - 3000
450,000
1000 - 2000
250,000
100 - 1000
100,000
50 - 100
50,000
25 - 50
25,000
< 25
500
Global Biodiversity Information Facility
GBIF Supplementary Fund
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Contributions may come from different
sources and may be targeted to specific
purposes
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Fund monies may be used:
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To assist developing countries in sending
delegations to Governing Board meetings
To help with infrastructure development
To further one or more of the Work Programme
areas
For any other purpose that furthers GBIF goals
Global Biodiversity Information Facility
GBIF Accomplishments to Date
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59 Participants have joined to date
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Secretariat established
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14 hired (via international searches) by Nov 2002
Moved into permanent quarters 5 Mar 2003
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Portal opened Mar 2003
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First version of information architecture in
place (by Dec 2003)
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DIGIT and ECAT seed money awards
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Training provided (DiGIR technologies)
Global Biodiversity Information Facility
More information about GBIF
www.gbif.org
Beatriz Torres: btorres@gbif.org
Phone: + 45 35 32 14 70
Fax: + 45 35 32 14 80
Global Biodiversity Information Facility