http://www.e-taxonomy.eu

Biodiversity information and cybertaxonomy:

International initiatives to inventory the earth's biodiversity (GBIF, Synthesys, Zoobank, EDIT,

EoL, SpeciesBase,...)

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Anne-Sophie ARCHAMBEAUGBIF FranceMNHN Géologie CP48 Phone:+33(0)14079806543 rue Buffon 75005 Paris mail: archambeau@gbif.fr

http://www.e-taxonomy.eu

Taxonomy Summer School1-15 September 2008

EDITPresentation title

Presenter’s positionPresenter’s name

Biodiversity information and cybertaxonomy: International initiatives

to inventory the earth's biodiversity

Communication officer at GBIF FranceAnne-Sophie Archambeau

Biodiversity Information: ● science that promotes the access, sharing and usage of data and knowledge concerning the biological diversity.

Taxonomy: ● naming, describing and classifying organisms● including all plants, animals and microorganisms of the world. ● taxonomists have named about 1.8 million species, yet the total number of species is unknown and probably between 5 and 30 million.

=> the aim is to combine these knowledge to inventory the earth's biodiversity and make it accessible on the web.

Creation and management of Systematic information systems:

From the field to the web: Needs in information systems at all the stages

From the knowledge to the representation of this knowledge:

Difficulties to transfer the information from the human brain to the computer’s processor

From the scientists to the wide audience Web effect: same data, different views

=> Development of international standards and projects to find better ways to answer these needs

Mid 60's : first computerization of a collection Ending 60's : Algorithms on key’s creation 1973 : First congress on Computer Assisted Indexing 1980 : DELTA (Description Language for Taxonomy)

1

1982 : First congress on Systematic data bases 1983 : XPER 1985: TDWG (Taxonomic Database Working Group),

attached as an IUBS commission in 1988

Chronology

Source: adapted from N. Bailly, 2004

TDWG : Taxonomic Database Working Group, now called Biodiversity Information Standards

www.tdwg.org

The aim: to establish international collaboration among biological database projects and facilitate data exchange, launched in 1985

Biodiversity Information Standards (TDWG) focuses on the development of standards for the exchange of biological/biodiversity data:

Develop, adopt and promote standards and guidelines for the recording and exchange of data about organisms

Promote the use of standards through the most appropriate and effective means and

Act as a forum for discussion through holding meetings and through publications

TDWG Working Groups Biological Descriptions Interest Group Geospatial Interest Group Imaging Interest Group Invasive Species Interest Group Literature Interest Group Natural Collections Descriptions Interest Group Observation and Specimen Records

Access to Biological Collections Data DarwinCore Task Group (DwC)

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Process Interest Group Taxonomic Names and Concepts Interest Group TDWG Architecture Group

Globally Unique Identifiers TAPIR Task Group

TDWG Infrastructure Project

www.tdwg.org

Authors of plant names Botanico-periodicum-huntianum Botanico-periodicum-huntianum/supplementum Economic botany data collection standard Floristic regions of the world Herbarium information standards and protocols for interchange of

data Index Herbarium, Part 1: The herbaria of the world International transfer format for botanic garden plant records Plant names in botanical databases Plant occurrence and status scheme Taxonomic literature ed. 2 and its supplements Users guide to the DELTA system World geographical scheme for recording plant distributions XDF: A language for the definition and exchange of biological data

sets

TDWG prior standards:

www.tdwg.org

TDWG current and draft standards:

TDWG Current (2005) Standards: Access to Biological Collection Data - version 2.06 Structured Descriptive Data Taxonomic Concept Transfer Schema

TDWG Draft Standards: TDWG Standards Documentation Specification TDWG Life Sciences Identifiers Applicability Statement

www.tdwg.org

Chronology 1988: FishBase Initiative 1988 : PANDORA 1992 : Earth Summit in RIO (prepared by UNEP since 1988)

(

Establishment of the Convention on Biological Diversity Clearing House Mechanism 1996-2000 : GTI Global Taxonomy Initiative

1993 : Systematics Agenda 2000 1993-1996: CDEFD (A Common Datastructure For

European Floristic Databases)

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1994: Species 2000

FishBaseFishBase is a global information system with all you ever wanted to

know about fishes and is one of the first and more complete taxonomic database. (since 1988)

FishBase is a relational database with information to cater to different professionals such as research scientists, fisheries managers, zoologists …

FishBase on the web contains practically all fish species known to science: ( 30300 Species, 266200 Common names, 46000 Pictures,41600 References, 1560 Collaborators, 23 million Hits/month )

FishBase was developed at the WorldFish Center in collaboration with the Food and Agriculture Organization of the United Nations (FAO) and many other partners, and with support from the European Commission (EC). Since 2001 FishBase is supported by a consortium of seven research institutions. FishBase is related to most of the international biodiversity initiative.

http://www.fishbase.org

United Nations Convention on Biological Diversity (CBD)

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Objectives Biodiversity conservation Sustainable use of its components Fair and equitable sharing of benefits arising from the

use of genetic resources. Organisation

COP Conference of the Parties SBSTTA Subsidiary Body for Scientific, Technical, and

Technological Advice Since 1993

www.cbd.int

CHM : Clearing House Mechanism (www.cbd.int/chm)

(

GTI : Global Taxonomy Initiative (www.cbd.int/gti): Confronting the taxonomic impediment to biodiversity conservation, launched in 1996

Remove the taxonomic impediment Reduce the lack of taxonomists Reduce the impact these deficiencies have on our

ability to conserve, use and share the benefits of our biological diversity.

Convention on Biological Diversity (CBD)

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www.cbd.int

Systematics Agenda 2000 (DIVERSITAS):Initiative emanating from biological systematists in the USA, in

1993, which proposes an intensive international programme over a 25 year period:

to discover, describe and inventory global species diversity to synthesize and produce phylogenesis and predictives

classifications to develop an appropriate information system to handle the

resulting information and provide dissemination of knowledge using data bases

Related to DIVERSITAS : international, non-governmental umbrella programme that would address the complex scientific questions posed by the loss of and change in global biodiversity. Launched in 1991 by United Nations Educational, Scientific and Cultural Organization (UNESCO), the Scientific Committee on Problems of the Environment (SCOPE) and the International Union of Biological Science (IUBS),

Chronology 1994 : European Science Foundation Systematics

Network 1994 : Tree of Life 1996 : OECD Megascience Forum Working Group on

Biological Informatics 1999-2001 : implementation of GBIF

(Global Biodiversity Information Facility)

(

1997 : OBIS (Oceanographical Biodiversity Information System)

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1997-1999 : BioCISE (Biologial Colletion Information System in Europe)

ToL : Tree of Life

http://tolweb.org/

Objectives: compiles information about biodiversity and the evolutionary relationships of all organisms (phylogeny):

To present information about every species and significant group of organisms on Earth, living and extinct,

To present a modern scientific view of the evolutionary tree that unites all organisms on Earth: ToL pages are linked to one another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project illustrates the genetic connections between all living things

To aid learning about and appreciation of biological diversity and the evolutionary Tree of Life.

To share information with other databases and analytical tools, and to phylogenetically link information from other databases.

http://www.iobis.org/

OBIS: Ocean Biogeographic Information System

Objectives: make marine biogeographic data, from all over the world, freely available over the World Wide Web.

OBIS provides: taxonomically and geographically resolved data on

marine life and the ocean environment; interoperability with similar databases; software tools for data exploration and analysis. 14 million records of 78000 species from 251 databases

OBIS working groups : Taxon names Working Group, Visualisation tools Working Group, Habitat classification Working Group, Fishery data Working Group, Discovery Metadata Working Group.

Chronology 1998-2004 : Access to infrastructures 1998-2000 : ERMS (European Register of Marine

Species)

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1999 : CoML (Census of Marine Life)

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1999 : First time that biodiversity as a domain was funded by the (5e) European Research Framework Programm (PCRDT, FP)

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2000 : FaEu (Fauna Europaea); EMP (Euro+Med PlantBase), ENHSIN (European Natural History Specimen Information Network)

S

European programms in taxonomic referentials:

The goal of these projects is to create a validated checklist of all the world's species in each domain: plants, animals, fungi and microbes:

List of valid species, List of validated common names, Establish the synonymy

They have been funded by the European Commission for a period of four years (1 March 2000 - 1 March 2004) within the Fifth Framework Programme (FP5).

European programms in taxonomicreferentials:

Flora Europaea + Mediflore -> Euro+Med PlantBase: www.emplantbase.org

ERMS (European Register of Marine Species) : www.marbef.org/data/erms.php

Fauna Europaea (FaEu): www.faunaeur.org Species 2000 Europa: European Catalogue of Life Project

www.sp2000europa.org/

Species 2000 is a "federation" of database organisations working closely with users, taxonomists and sponsoring agencies.

The website provide a validated checklist of all the world's species (plants, animals, fungi and microbes). This is being achieved by bringing together an array of global species databases covering each of the major groups of organisms.

Species 2000

www.sp2000.org

Integrated Taxonomic Information System

www.itis.gov

ITIS provides authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world.

=> In 2001, Species 2000 & ITIS decided to work together to create the Catalogue of Life (CoL).

The Catalogue of Life provides the taxonomic backbone to the GBIF and the Encyclopedia of Life (EOL).

Catalogue of Life (CoL)

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Objectives: Comprehensive catalogue of all known species of organisms on Earth by the year 2011.

The Catalogue is published as two products: Annual Checklist : fixed edition that can be cited and used as a

common catalogue for comparative purposes by many organisations. CD-ROM and on the website. The seventh edition of the Annual Checklist contains 1,008,965 species.

Dynamic Checklist: virtual catalogue operated on the Internet and available both for users and as an electronic web-service. The Dynamic Checklist harvests taxonomic sectors and associated strands of hierarchical classification dynamically from the source databases across the internet.

http://www.catalogueoflife.org/

Chronology 2000-2002 : All Species Foundation March 2001: GBIF Established 2001 : BioCASE (A Biodiversity Collection Access

Service for Europe) FP5 2002 : Earth Summit in Johannesburg 2003 : ENBI (European Network for Biodiversity

Information) FP5 2003 : EuroCat (Species 2000 Europe)

2

2003 : 6e PCRDT/ FP6

Biological Collection Access Services

BioCASE: transnational network of biological collections of all kinds.

Objectives: widespread unified access to distributed and heterogeneous European collection and observational databases using open-source, system-independent software and open data standards and protocols.

BioCASE provides BCI: the Biodiversity Collections Index online. (www.biodiversitycollectionsindex.org/static/index.html)

www.biocase.org

GBIF: Global Biodiversity Information Facility

main objectives and achievements in an international framework

www.gbif.org

... make the world’s scientific biodiversity data freely and universally

available via the Internet.

GBIF's mission :

to establish a distributed information infrastructure that serves primary biodiversity data

with initial focus on species- and specimen-level data,

with links to ecosystem, ecological, molecular and genetic levels

GBIF’s work is fully in line with the Convention on Biological Diversity (CBD) -> GTI, GSPC, Protected Areas, Invasives, 2010 target and CHM

GBIF's objectives are :

● June 1999: OECD Science Ministers (CSTP) endorsed GBIF, and recommended it be established as independent organization

1 March 2001: GBIF established 19 countries and organisations as founding members

June 2001: Copenhagen selected to host GBIF Secretariat

February 2002: GBIF Secretariat operational February 2004: GBIF data portal online July 2008:

+ 140 million records are online 81 countries and organisations

GBIF history :

GBIF’s focus: biodiversity datas

Existing responsibilities of other groups

GBIF's place among international organizations:

GBIF avoids duplication of effort

Partnerships are vital to GBIF

Works to maximize benefits to all

Can contribute to science, policy and applications

What primary data exists?

1-3 billion physical specimens in museums

Label data to be digitised 250-400 million digital data

records off-line Museums, observation

networks, natural resource surveys, etc.

+140 million records are online today through GBIF

Using agreed standard, formats

Benefits of mobilizing data:

Recognition of importance of collections and higher visibility of the institution or research project as useful to society Global dissemination of the data Source of the data gets credit when used

Better management (supported by scientific data) of biological resources,

Public understanding of the contributions of scientists to society, and biodiversity itself

GBIF Operational Areas :

Network and Nodes Implementation: Providing best practices and models for Participants to build and run their GBIF nodes

Data Access and Database Interoperability (DADI): Developing standards for linking biodiversity databases, Serving linked data through a common data portal

Digitization (DIGIT):Digitising primary biodiversity data Electronic Catalog of Names of Known Organisms

(ECAT): Developing a list of the scientific and common names of all 1.8 million known species

Outreach and Capacity Building (OCB): helping countries and organizations to share and use biodiversity data

Everything GBIF does is in partnership with others

2010 Indicators, GTI, GSPC, CHM

Global Biodiversity Information Facility

International ProgrammesInternational Programmes

TDWG

CDEFD BioCISE

ENHSIN

Tree of Life

ITIS

GBIF will enable synergism among existing investments that is not possible at present

+ Network of GBIF natl. nodes / IPR / Products / e-Services / Portal

GBIF GBIF TopicsTopics and and ProgrammesProgrammesContent area responsibilities of GBIFContent area responsibilities of GBIF

FishBase

Common AccessInteroperability

BiodiversityLiteratureResources

Search Engines

Catalogue of namesof known organisms

BiologicalSpecimen Data

Species bankTaxa description

Outreach andCapacity building

TDWG

ABCDSDD

Names

ECATDIGIT OCB

DADI

DiGIRAll Species

OBIS/CoMLe-Types

RefTax

BioInfoSimbio

ArcBota

TB-HFGECO

RIHA

SPN

ENBI: European Network for Biodiversity Information

FaEu

EMP

BioCASE EuroCat

ERMSENHSIN

CDEFD

BioCISE

Synthesys

DiGIRENHSIN

BioCASE EuroCat

Catalogue of LifeSpecies2000-

OctopusSPP

ITIS

GBIF’s achievements to date ... Data Portal (http://data.gbif.org): + 140 million

biodiversity data available. Capacity Building: training sessions (English,

French,Spanish). Puting data to use: Data modeling workshops

Mentoring Program: To support building up NODES and foster N-N, S-S and N-S collaboration.

Demo Projects: develop protypes, proof of concept and applications.

Active pursuit of data repatriation

Biodiversity and information about it are unevenly distributed….

holder of large amounts of biodiversity databiodiversity hotspot

http://http://data.gbif.orgdata.gbif.org

Which kind of information can be found in the GBIF?

Data on species occurrences (based on specimens or observations)

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What ? Where ?

Names Scientifics names & classification Common names

When ? By who ?

Different ways to find the information 2. Searching by words

1. Explore directly

3. Advanced search

http://data.gbif.orghttp://data.gbif.org

Use of thedata portal:

click here

Which species are presents in a country?

1. Choose the initial’s country

2. Choose the country in the list

Be careful: • The list of species

may be not complete

• GBIF needs more contents

Which species are presents in a country?

ActionsThis box

gives the options of

uses

Summary of results

Which species are presents in a country?

Obtain list of species based on the network information

Download the information in diverse format for different usages

Find the datasets which contains information on that country

Which species are presents in a country?

Which are the dataproviders who give information on a country?Which are the dataproviders who give information on a country?

Choose the datasets you want to see with the boxes