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Two use cases to accelerate biodiversity research are now operational
Press Release, December 2012
Taxonomic information classifying names of species is essential for reliable environmental science, for monitoring changes in biodiversity and for effectively addressing global challenges related to environmental change. But accessing and using taxonomic information is far from easy as we cannot always be sure that the same taxonomic name will appear in different catalogues, refer to the same species, or even appear at all.
“One major problem is integrating regional taxonomies that have been created locally for regional floras and faunas with global taxonomies linked to worldwide monographs and species databases” explains Alex Hardisty, Director of Informatics Projects, Cardiff School of Computer Science and Informatics, Cardiff University. “The ability to cross-reference between regional and global taxonomic data sets is often masked by complex differences in the taxonomic classification used. A species may, for instance appear to be missing from one catalogue because it is subsumed within another species in the other catalogue”.
EUBrazilOpenBio project is addressing barriers such as this by making user-friendly tools more widely available to specialists in Brazil and Europe. EUBrazilOpenBio deploys a joint EU-Brazil cloud computing based e-infrastructure of open access resources that allows sharing of hardware, software and data on-demand for the benefit of EU and Brazilian biodiversity scientific communities, data and resource managers.
Two use cases demonstrating biodiversity research are now operational and available to the community. One of the use cases focuses on comparing regional and global taxonomies. It cross-maps the regional List of Species of Brazilian Flora, containing around 10,000 species organized under 40,000 plant taxa names (including synonyms), against the global Species2000/ITIS Catalogue of Life (CoL), indexing about 150,000 plant species. The CoL Cross-mapping Tool developed by Cardiff University helps manage differences between catalogues by detecting, analysing and reporting not only differences between two checklists of species, but also differences in their taxonomic treatment. It identifies potential resolutions to help taxonomists resolve these differences.
The idea is to benefit from the “taxonomic intelligence” of the Tool and support a pilot study that analyses the regional plant catalogue of Brazil against the global index of plants within the CoL. This will be used to improve the linkage between the terms in the lists and to enahance both the CoL and the Brazilian List of Flora. This will allow taxonomic and biodiversity specialists to utilise richer data. Over time it will also lead to a better understanding of the differences, swopping information in both directions (from regional taxonomy to the Catalogue of Life and vice-versa); thus helping to fill and close gaps between different taxonomies. This will help scientists using these lists to obtain a fuller picture of information about species they are researching (e.g. in Species Distribution Modelling)
In addition to this collaborative work, EUBrazilOpenBio is building on the on-going efforts of the Brazilian National Institute of Science & Technology – Virtual Herbarium of Flora and Fungi. Using a standard procedure for plant species native to Brazil, the aim is to generate species distribution (or ecological niche) models based on specimen data. This requires interaction with the List of Species of the Brazilian Flora with around 40.000 plant names in its 2010 edition, and with the speciesLink network, currently providing almost 5 million species occurrence records from hundreds of institutions. The modelling procedure uses different algorithms and separate steps for model assessment and projection into different environmental scenarios.
“Our cooperation with the Brazilian Virtual Herbarium is also part of the drive towards a more complete and integrated view, identifying knowledge gaps in the biogeography of flora and using herbarium data to generate ecological niche models”, says Vanderlei Canhos, Director of the Reference Centre on Environmental Information (CRIA) in Brazil and EUBrazilOpenBio Brazilian Coordinator.
The cross-mapping tool and the ecological niche modelling tool are available from the EUBrazilOpenBio Gateway, the project open-access platform where existing European and Brazilian infrastructures and resources are integrated. The EUBrazilOpenBio Virtual Research Environment provides access to the two main project use cases.
Sara Pittonet Gaiarin