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i4Life: Standardising the World’s Biodiversity Catalogue
A Culham, M Sitko, Y Roskov, V Didziulis, K Cheung, T Kunze, P Schalk, W Addink, M Doring, G Cochrane, S Riviere,V Robert, W Bogdanowicz, C Hilton-Taylor, W Berendsohn, A Guntsch, A Jones, R White, T Bourgoin IST-Africa 2013 Conference Proceedings 2013
i4Life provides linkages between the Catalogue of Life, an expert based knowledge portal for living species on earth, and global partners (IUCN, GBIF, ENA at EBI, BOLD, EoL, and Life Watch) providing data portals for distribution, genetic diversity and conservation information. This novel e-infrastructure offers the only single global consensus list of living species on earth and their associated data. This
structure uses custom services to cross-map, transfer, and make available subsets of this global list to interested users. It facilitates both global and local understanding of biodiversity, it’s distribution, variation and threats.
Identifying and Relating Biological Concepts in the Catalogue of Life
AC Jones, RJ White and ER Orme Journal of Biomedical Semantics 2011.2:7
Background: In this paper we describe our experience of adding globally unique identifiers to the Species 2000 and ITIS Catalogue of Life, an on-line index of organisms which is intended, ultimately, to cover all the world’s known species. The scientific species names held in the Catalogue are names that already play an extensive role as terms in the organisation of information about living organisms in bioinformatics and other domains, but the effectiveness of their use is hindered by variation in individuals’ opinions and understanding of these terms; indeed, in some cases more than one name will have been used to refer to the same organism. This means that it is desirable to be able to give unique labels to each of these differing concepts within the catalogue and to be able to determine which concepts are being used in other systems, in order that they can be associated with the concepts in the catalogue. Not only is this needed, but it is also necessary to know the relationships between alternative concepts that scientists might have employed, as these determine what can be inferred when data associated with related concepts is being processed. A further complication is that the catalogue itself is evolving as scientific opinion changes due to an increasing understanding of life.
Results: We describe how we are using Life Science Identifiers (LSIDs) as globally unique identifiers in the Catalogue of Life, explaining how the mapping to species concepts is performed, how concepts are associated with specific editions of the catalogue, and how the Taxon Concept Schema has been adopted in order to express information about concepts and their relationships. We explore the implications of using globally unique identifiers in order to refer to abstract concepts such as species, which incorporate at least a measure of subjectivity in their definition, in contrast with the more traditional use of such identifiers to refer to more tangible entities, events, documents, observations, etc.
Conclusions: A major reason for adopting identifiers such as LSIDs is to facilitate data integration. We have demonstrated the incorporation of LSIDs into the Catalogue of Life, in a manner consistent with the biodiversity informatics community’s conventions for LSID use. The Catalogue of Life is therefore available as a taxonomy of organisms for use within various disciplines, including biomedical research, by software written with an awareness of these conventions.
Publications that have cited us:
An appraisal of megascience platforms for biodiversity information
D Triebel , G Hagedorn, and G Rambold MycoKeys 2012 5:45–63
The megascience platforms Biodiversity Heritage Library (BHL), Catalogue of Life (CoL), Encyclopedia of Life (EOL), Global Biodiversity Information Facility (GBIF), International Barcode of Life (iBOL), International Nucleotide Sequence Database Collaboration (INSDC) and JSTOR Plant Science, all belong to a group of global players that harvest, process, repurpose and provide biodiversity data on all kinds of organisms. Each of these platforms primarily focus on one data domain, for instance, taxonomy and classification, occurrence, morphology, ecology, and molecular data.
The present contribution describes aspects of processing and provision of biological research data on these platforms, focusing on the technical implementation of data exchange, copyright issues, and data sharing policies as well as their implications for data custodians, owners, providers, and publishers. With the exception of JSTOR Plant Science, most international initiatives seek long-term business models and funding mechanisms to provide online data openly and free of charge. For example, currently GBIF depends on governmental commitments for its funding, and CoL is financed by EU or national grants, as well as being based on Species 2000, a British non-for-profit company, and ITIS. These business models are compared with that of JSTOR Plant Science, the commercial portal of the Global Plant Initiative (GPI). All initiatives currently meet challenges of sustainability with regard to data curation as well as software development for maintaining the complexity of their services. All platforms discussed here also harvest and provide mycological and lichenological research data.
Can We Name Earth’s Species Before They Go Extinct?
MJ Costello, RM May, NE Stork Science 2013; 339, 413
Some people despair that most species will go extinct before they are discovered. However, such worries result from overestimates of how many species may exist, beliefs that the expertise to describe species is decreasing, and alarmist estimates of extinction rates. We argue that the number of species on Earth today is 5 ± 3 million, of which 1.5 million are named. New databases show that there are more taxonomists describing species than ever before, and their number is increasing faster than the rate of species description. Conservation efforts and species survival in secondary habitats are at least delaying extinctions. Extinction rates are, however, poorly quantified, ranging from 0.01 to 1% (at most 5%) per decade. We propose practical actions to improve taxonomic productivity and associated understanding and conservation of biodiversity.