Tuesday, 22 October 2013

i4Life Part 5: Global Biodiversity Partners

Global Biodiversity Programmes

Previous posts in this series:
Part 1: Improving the world's taxonomic data indexing
Part 2: Global Species Databases
Part 3: The Catalogue of Life

In the last post we looked at how the Catalogue of Life shares its data with partners and collaborators through the Download Tool and Web Services. So who are the Catalogue of Life's partners and collaborators? Well the Catalogue of Life is itself a partnership between the officiating ITIS and Species 2000 organisations and the confederation of 139 contributing expert-curated taxonomic databases. But now, as a result of the i4Life project the collaborative reach has grown even further to include leading global biodiversity programmes and international research groups.

Today the Catalogue of Life is used as a common index for taxa in the catalogues of five global biodiversity programmes - IUCN Red List, Global Biodiversity Information Facility, European Nucleotide Archive, Barcoding initiatives and Encylopedia of Life. This index has acted as a backbone for a growing harmonisation between these catalogues, making it possible to share more easily names that are present and identify those missing in each. This process also includes the recognition of data stored under synonymic names, because in addition to 1.4M plus species names held, the Catalogue of Life currently contains over a million synonyms too. This allows partners to enhance their own catalogues by including names from the Catalogue of Life that they do not have, meaning a more comprehensive taxon search can be conducted by users in each of their own data portals. Through the Piping Tool (our next post!) the Catalogue of Life can receive names from partners that it doesn't hold, but can only include them once they have been assessed by taxonomic experts of the contributing Global Species Database (GSD) for that taxon. Once placed (or not), updated GSD checklists are then sent back to the Catalogue of Life for inclusion in the next edition of the Dynamic checklist, before once again being made available to partners through the Download and Web Services. Many of the additional names that are circulating may be synonyms or even misspellings, but until this i4Life data flow is complete it is not possible to know exactly how many valid species names that constitutes. Names that the Catalogue of Life is missing, while probably a small fraction of the total are highly significant. While the Catalogue of Life is the largest expert-curated species indexing mechanism currently out there, if it can not index all names global biodiversity programmes hold, its taxonomy is not as useful to partner programmes as it otherwise would be. However, the lack of Global Species Databases for some taxa means this is an incremental rather than an exhaustive process. Through i4Life the e-infrastructure is now in place to keep this data flow moving. In the meantime, the Catalogue of Life, global biodiversity programmes and Global Species Databases are all enhancing the quality of their data and for the end user this will mean more agreement across data portals and less confusion.

It has been no easy task establishing this exchange, both setting up these global partnerships, and agreeing appropriate methods to make sharing species information as painless as possible. That is in addition to the actual development of the e-infrastructure and making it operational and sustainable. But today, the Catalogue of Life now delivers a refreshed instance of the Catalogue of Life taxonomy in an internationally recognised data exchange format (a key achievement of i4Life) on a monthly basis for use in the heterogeneous catalogues and portals of global biodiversity programme partners. This level of networking, cooperation and integration demonstrates the level of commitment in the biodiversity community to shared goals and a desire to achieve them collectively.

Below is a brief overview of what the global biodiversity programmes are that form i4Life's Global Biodiversity Partners, and how they are exploring or aggregating different aspects of biodiversity knowledge that includes global species distribution modelling, genome and sequence diversity, species identification using DNA Barcodes and conservation status. What is common among them all is the need for a taxonomic index from which all their other data can radiate - this is where the Catalogue of Life comes in. For more information please find a link to each of their data portals.

IUCN Red List
The IUCN Red List is a database of information related to a species risk of extinction and conservation needs. Information is presented at the species level and therefore the Red List has at its core, a taxonomic backbone. It is now widely recognised as one of the fundamental tools to support conservation planning, management, monitoring, and decision making, with among other things growing value for broadening and strengthening our understanding of human impact on biodiversity.


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 through aggregation of their data. It also serves many different communities. The richness and importance of its biodiversity data, in particular its distribution data, is widely used 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 taxonomy feeds into the GBIF infrastructure.


European Nucleotide Archive (ENA)
The European Nucleotide Archive provides a comprehensive, accessible and publicly available repository for nucleotide sequence data. Nucleotide sequence information is crucial to our understanding of biology, from genetics and molecular interactions through to organism-wide processes. Free access to nucleotide sequence data is therefore essential for life science research. As large-scale sequencing becomes faster and cheaper, the need to deposit, search and analyse information in a central archive that is publicly available and easily accessible continues to grow.


Barcoding Initiatives
The various “barcoding of life” initiatives like BOLD, CBOL, ECBOL, iBOL or QBOL are currently some 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 identify existing taxa and new tools are currently under development to discover the vast majority of the species biodiversity that remains unknown. In 2004, CBS-KNAW launched the Mycobank initiative, introducing new standards and methods for the deposit and the registration of new species names and associated data. Unlike existing species registration systems, it can handle nomenclatural, taxonomical, geographical, bibliographical, morphological, physiological, chemical, electrophoretic and other molecular data.

Website (Mycobank)

Encyclopedia of Life (EoL)
The goal of the Encyclopedia of Life is to compile and make available over the Internet as much information as possible about the world’s species of plants, animals and microorganisms. It started as 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 - and includes a role for the general public and other international partners too.


Next up: Piping Tool

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