Contributors

 

 

Organisation

The Catalogue of Life is led by Species 2000, working in partnership with ITIS:

In June 2001 the Species 2000 and ITIS organisations, that had previously worked separately, decided to work together to create the Catalogue of Life, now estimated at 1.9 million species (Chapman, 2009). The two organisations remain separate and different in structure. However, by working together in creating a common product, the partnership has enabled them to reduce duplication of effort, make better use of resources, and to accelerate production. The combined Annual Checklist has become well established as a cited reference used for data compilation and comparison. For instance, it is used as the principal taxonomic index in the GBIF and EoL data portals and recognised by the CBD.

The scientific policy for the Catalogue of Life programme is developed by the CoL Global Team: David Eades (Convenor, USA), Tom Orrell (USA), Richard Pyle (USA), Mike Ruggiero (USA), Richard White (UK), Jeya Kathirithamby (UK), Alastair Culham (UK), Jerry Cooper (New Zealand), Mark Costello (New Zealand), Nicolas Bailly (Philippines), Thierry Bourgoin (France), Christina Flann (The Netherlands), Li-Qiang Ji (China), Patricia Mergen (Belgium), Heimo Rainer (Austria), Tony Rees (Australia), with further assistance from the Regional Hubs.

Species 2000 is an autonomous federation of taxonomic database custodians, involving taxonomists throughout the world. The goal is to collate a uniform and validated index to the world's known species. Species 2000 is registered as a not-for-profit company limited by guarantee (registered in England No. 3479405) with six directors, and taxonomic database and relevant software organisations from around the world as members. It started from a TDWG Task Group; sponsored by CODATA, IUBS and IUMS; is an associate participant in GBIF, a data provider to EC LifeWatch; and is recognised by UNEP and the CBD. Its Phase II Programme includes EC 4D4Life and i4Life e-infrastructure projects (see below). 4D4Life included the establishment of a Global Multi-Hub Network with Regional Centres in China, New Zealand, Australia, Brazil and N. America. i4Life includes pipelines for data exchange and checklist harmonisation with GBIF, EBI/NSDC, Barcode of Life, IUCN Red List and EoL.

Species 2000 is governed by an elected Board of Directors that deals with legal and financial matters, and that is advised by the CoL Global Team on scientific policy. The Directors are presently: Peter Schalk (Chair, The Netherlands), Alex Gray (UK), David Eades (Convenor of the CoL Global Team, USA), Guy Baillargeon (Canada), Vanderlei Canhos (Brazil) and Keping Ma (China).

The Integrated Taxonomic Information System (ITIS) is a partnership of federal agencies and other organizations from the United States, Canada, and Mexico, with data stewards and experts from around the world (see www.itis.gov). The ITIS database is an automated reference of scientific and common names of biota of interest to North America and includes global treatment for many groups. ITIS contains more than 762,000 scientific and common names in all kingdoms, is accessible via the World Wide Web in English, French, Spanish, and Portuguese (itis.gbif.net) and is an associate member of GBIF. ITIS supplies both global and New World groups to the Catalogue of Life – with emphasis on GSDs.

ITIS is managed by Gerald Guala (Director), Thomas Orrell (Deputy Director), Michael Ruggiero (Senior Scientific Advisor), David Nicolson (Data Development Leader), Mike Frame (Information Technology Leader), Roy McDiarmid (Taxonomy Leader), James Macklin (ITIS-Canada Director), and Patricia Koleff (SIIT-Mexico Director). They are advised and supported by the ITIS Steering Committee and ITIS Data Stewards.


 

 

Taxonomic Opinion

The Catalogue of Life provides an integrated, simplified perspective on taxonomy:

Peer review, undertaken by three independent experts, will establish whether a database is of sufficient quality to address a specific gap in the Catalogue.

The Catalogue is structured around a management classification, which provides a robust hierarchy for all species. The development of the management classification, and its relationship to various competing views of evolutionary relationship, is discussed by Dennis Gordon in a paper published with the Catalogue. Read more

Within a contributing Global Species Database, the taxonomic structure reflects the opinion of its custodian; each Database is attached within the management classification at a single node.

 

 

Global Species Database Partners

The Catalogue of Life depends upon the contributions of more than 130 Global Species Databases:

Global Species Databases are established at centres of expertise around the world, and the task continues to identify data sources that address gaps in the Catalogue.

Global Species Databases are validated for inclusion by independent peer review, ensuring that the best available sources are identified. A few of the datasets contain data only for specific regions, where global coverage has not yet been achieved: these are clearly identified in the data. Completeness of data within individual databases is indicated within the dataset, based upon an assessment by the contributor.

The source databases are diverse in their origin, their purpose and therefore their structure. A key challenge for the Catalogue of Life has been the integration of this disparate data, and a standard dataset has been established for that purpose.

Global Species Databases aspire to the following properties:

  • cover one taxon worldwide
  • contain a taxonomic checklist of all species within that taxon
  • deal with species as taxa, and contain synonymy and taxonomic opinion
  • have an explicit mechanism for seeking at least one responsible / concensus taxonomy, and applying it consistently
  • cross-index significant alternative taxonomies in their synonymy

 

 

Regional Centre Partners

For some of the least well-known groups of organisms, no one is creating global species databases:

However, complete databases are being created at regional level, and these have particular significance in the mega-diverse regions.

A key element of the development programme for the Catalogue of Life (through originally the EU Framework 7 4D4Life project) is modelling the future integration of these major regional centres.

 
Europe

Species 2000 Europa (2003-2006) provided the opportunity for developing the concept of regional hubs, and for building a prototype with EuroCat, the European complete regional checklist.

The checklist established the principle of collating a distributed array of existing taxonomic databases, each enhanced on a continuing basis by taxonomic experts. It established the means to look up biological information, essential classification and accepted names, synonyms, and common names of any species. That distributed array continues as an integrated function of the Catalogue of Life.

 
North America

ITIS is the North America node of Species 2000 is provided by ITIS, and funded by the US Federal Government. It is based at the Smithsonian Institution and is a partnership designed to provide consistent and reliable information on the taxonomy of biological species, with Canadian and Mexican government agencies participating. The primary focus of ITIS is North American species, but many groups are worldwide.

ITIS also partners Species 2000 with the common goal to create the Catalogue of Life.

 
China

Species 2000 China Node was established in 2006 by the Biodiversity Committee of the Chinese Academy of Sciences, through the Institute of Botany and Institute of Zoology CAS. Annual editions of the Catalogue of Life China have been published since 2008, which is an important data source for the CoL annual checklist since 2013(?).

 
New Zealand

New Zealand Organisms Register (NZOR), is nationally funded at LandCare Research, a Crown Institute.

Landcare Research is one of nine independent Crown Research Institutes founded in 1992, and is New Zealand’s leading provider of solutions and advice for sustainable development and the management of land-based natural resources.

 
Brazil

Catalogo da Vida Brasil , is in development by CRIA in Campinas, working with the Brazilian Ministry of Science & Technology.

The aim of CRIA (Reference Center on Environmental Information) is to contribute towards a more sustainable use of Brazilian biodiversity through the dissemination of high quality scientific information to support policy and decision-making, and to promote education for sustainable development. CRIA's activities are focused on the development of information systems for the dynamic integration and visualization of biodiversity data from distributed information resources.

 
Australia

Atlas of Living Australia (ALA) is a federally funded programme at CSIRO (Entomology), in partnership with the Australian Biological Resources Study (ABRS).

ABRS is part of the Parks Australia Division of the Commonwealth Department of the Environment, Water, Heritage and the Arts. It was established to coordinate research in taxonomy and document the flora and fauna of Australia and is Australia’s national focal point for taxonomy.

ALA is a partnership of Australian scientific institutions and organisations, and is developing a data management system to catalogue and organise information relevant to the study of Australia’s biodiversity. The project will bring together information from a wide variety of sources, including many of the country’s most significant natural history collections and herbaria, ecological and observational data sets, images, online literature, diagnostic tools and molecular data.

 

 

Funding & Support

Content and infrastructure for the Catalogue of Life have was built with funding from 4D4life. Content, infrastructure and outreach are being enhanced with funding from i4Life, and further support for the secretariat of Species 2000 has been provided by OpenBio.

 

4D4Life (Dynamic Distributed Databases for Life)

A Scientific Data Infrastructures Project (2009-2012) of the European Commission's e-Infrastructure Programme, itself part of the Capacities Programme of Framework 7.

4D4Life established the Catalogue of Life as a state of the art e-science facility based on an enhanced service-based distributed architecture. This makes it available for integration into analytical and synthetic distributed networks such as those developing in conservation, climate change, invasive species, molecular biodiversity and regulatory domains. The project strengthened the development of Global Species Databases that provide the core of the service, and extended the geographical reach of the programme beyond Europe. Service Activities, the largest part of 4D4Life, created new electronic taxonomy services, including synonymy server, taxon name-change, and download services.

 

i4Life (Indexing for Life)

A European e-Infrastructure project, co-funded by the European Commission’s Seventh Framework Programme for Research and Technological Development. The project was launched in 2010. i4Life is a continuation and expansion of the 4D4Life project.

i4Life has one principal goal – to provide tools for the comparison and harmonisation of the various species catalogues used by six global biodiversity programmes using the Catalogue of Life as a yardstick. This goal will be achieved by the establishing of a virtual research community that will interlink and harmonise the taxonomic catalogues presently used by each of the global partners and to create an enhanced list of the entire set of organisms.


 

Open Bio

OpenBio aims to combine the Biodiversity Science and the Open Access Movement, promoting the concept of the openness for scientific research. The project will deploy an open-access platform from the federation and integration of existing European and Brazilian infrastructures and resources, making significant strides towards fully supporting the needs and requirements of the biodiversity scientific community.

EUBrazilOpenBio (288754) is a Small or medium-scale focused research project (STREP) funded by the European Commission under the Cooperation Programme, Framework Programme Seven (FP7).

 

 

Prof. Frank Bisby 1945-2011


Prof Frank Bisby 1945 - 2011

The Catalogue of Life was the driving vision of Frank Bisby, its founder and champion. Frank was a leader in the global communication of taxonomy and biodiversity informatics and a passionate advocate for his science.  He had a profound impact on this international effort to catalogue the world's species.

 

Obituary, published by Prof Vernon Heywood in
Flora Mediterraneana 21: 345-353 (2011).

 

 

 

Global Partner Programmes


The Catalogue of Life is evolving to provide an effective partner to six global biodiversity programmes (through the i4Life European e-Infrastructure project, 2010-2013), creating an ecosystem of services. The Catalogue is able to support the needs of these partner programmes in establishing validated taxonomy, and moreover share a variety of related services amongst all.

 

 
Global Biodiversity Information Facility (GBIF)

GBIF is a distributed and digital infrastructure which builds upon the collective efforts of and contributions of thousands of scientists in hundreds of institutions across the world. It is also serves many different communities. The richness and importance of this data is recognised widely by different organisations in science and society. The Convention on Biological Diversity and other international conventions, land-use planners and the agricultural sector, are all asking for new services which GBIF can help to deliver. The Catalogue of Life feeds into the GBIF infrastructure.

The taxon portal in GBIF. GBIF's mission is to make the world’s biodiversity data freely and universally available via the Internet. As a megascience initiative, GBIF aims to provide an essential global informatics infrastructure for biodiversity research and applications worldwide. The GBIF primary biodiversity data store provides an index of over 300 million data records from over 10,000 different databases.

Catalogue of Life has provided a standard dataset to GBIF since 2007.

 

 

 
Barcode of Life Data Systems (BOLD)

The various “barcoding of life” initiatives like the Consortium for the Barcode of Life (CBOL), the European Consortium for the Barcode of Life (ECBOL), The International Barcode of Life project (iBOL) or the Quarantaine Barcoding of Life proje (QBOL) are currently one of the major sources of new species. BOL projects and principles are helping scientists to discover substantial numbers of cryptic species. New tools have been created to help identifying existing taxa and new tools are currently under development to discover the vast majority of the species biodiversity that remains unknown.

BOLD - The Barcode of Life Data Systems is an online workbench that aids collection, management, analysis, and use of DNA barcodes. It consists of 3 components (MAS, IDS, and ECS) that each address the needs of various groups in the barcoding community.

The specification for the BOLD/ECBOL pipeline has been established.

 

 

 
IUCN Red List

The IUCN Red List is widely recognized as one of the fundamental tools to support conservation planning, management, monitoring, and decision making, with growing value for, among others:

  • broadening and strengthening our understanding of human impact on biodiversity;
  • helping to track progress towards major global biodiversity-related targets;
  • influencing globally flexible conservation spending; and 4) demonstrating the importance and value of biodiversity to society.

The IUCN Red List is fundamentally a database of information related to species risk of extinction and conservation needs. Information is presented at the species level and therefore the Red List has a taxonomic backbone at its core.

The IUCN Red List profiles over 47,000 species and is growing each year.

A pipeline is being developed to transmit Catalogue of Life updates to IUCN, and additional IUCN Red List name data to the Catalogue. A cross-mapping process is also being established to relate the two taxonomic systems.

 

 

 
Encylopedia of Life

The goal of the Encyclopedia of Life (EOL) is to compile and make available over the Internet as much information as possible about the world’s species of plants, animals and microorganisms. A collaborative effort involving several of the world’s leading science institutions—Harvard University, the Field Museum, the Marine Biological Laboratory, the Smithsonian Institution, the Biodiversity Heritage Library, and the Missouri Botanical Garden.

EOL expects that it will take ten years to gather basic information on all 1.9 million species of extant organisms.

The Encyclopedia of Life uses the Catalogue of Life Annual Edition as its taxonomic backbone.

 

 

 
EMBL Euopean Nucleotide Archive (ENA)

The longest running nucleotide archive collaboration, the International Nucleotide Sequence Database Collaboration (INSDC), has been underway for over a quarter of a century and now serves as a model for data sharing in the life sciences.

Amongst the European Bioinformatics Initiative (EBI) data services, it is the European Nucleotide Archive (ENA) that harbours data from the largest range of organisms. Each of approximately 300,000 species names is associated with at least one archival nucleotide sequence record. Complete genome services at EBI have greatly limited organism coverage; we know about 4,500 completed and ongoing sequencing projects. Following the route of biological information from genomic nucleotides through transcription, translation, protein interactions, pathways and whole systems, organism coverage rapidly drops. The ENA uses the taxonomic classification of organisms that is maintained at NCBI, but through INSDC has strong collaboration with the group such that newly found organisms are classified as sequence is submitted.

ELIXIR is an EU-funded programme to construct and operate a sustainable infrastructure for biological information in Europe to support life science research and its translation to medicine and the environment, the bio-industries and society. Building the Catalogue of Life pipeline to the ENA provides a basis upon which the taxonomic infrastructure of ELIXIR may be built.

A pipeline is being developed to transmit Catalogue of Life updates to EBI, and additional EBI name data to the Catalogue. A cross-mapping process is also being established to relate the two taxonomic systems.

 

 

 
Lifewatch

The LifeWatch infrastructure for biodiversity research will support the development of integrated, large-scale data resources, advanced analytical and modelling capabilities with computational power. LifeWatch will not only serve the scientific community, but will also be an essential tool for local and global policy makers in the understanding and the rational management of our ecosystems. It draws upon a previous programme, EDIT.

Edit The European Distributed Institute of Taxonomy (EDIT) was built as the collective answer of 29 leading European, North American and Russian institutions to a call of the European Commission, issued in 2004, for a network in 'Taxonomy for Biodiversity and Ecosystem Research'. The EDIT consortium agreement started in 2006 and lasted 5 years. The EDIT cyberplatform is planned for integration as a component of the LifeWatch Virtual Laboratory.

A pipeline for transmitting Catalogue of Life updates to the EDIT cyberplatform is under development