OpenBioEU-Brazil

EU-Brazil Open Data and Cloud Computing e-Infrastructure for Biodiversity

www.eubrazilopenbio.org

European CommissionInformation Society and Media

Esse projeto é resultante do Edital MCT/CNPq Nº 066/2010 - Programa de Cooperação Brasil – União Europeia na Área de Tecnologias da Informação e Comunicação – TIC.

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)

EUBrazilOpenBio is a collaborative initiative addressing strategic barriers in biodiversity re-search by integrating open access data and user-friendly tools widely available in Brazil and Europe. EUBrazilOpenBio deploys a joint EU-Brazil cloud-based e-infrastructure that allows the sharing of hardware, software and data on-demand. Biodiversity scientists can use these open access resources and the applications developed by the project to conduct a wide range of conservation and research programmes. The EUBrazilOpenBio e-Infrastructure development is being guided by two Use Cases. The first one focuses on comparing regional and global taxonomies,  such as the regional List of Species of Brazilian Flora against the global Species2000/ITIS Catalogue of Life, helping ta-xonomists to manage differences between catalogues and in the taxonomic treatment of spe-cies. The second use case builds on work by organisations such as the Brazilian Virtual Herba-rium of Flora and Fungi to facilitate the generation of niche models that predict the potential distribution of species under different environmental conditions.

Technologies and Data Resources

EUBrazilOpenBio integrates dif-ferent technologies to make a large variety of services avai-lable for managing, manipulating and processing data and metada-ta within an autonomously-ma-naged infrastructure: gCube sy-stem, openModeller, COMPSs, EasyGrid AMS, VENUS-C, HTCon-dor, u.store

EUBrazilOpenBIo leverages on existing European, Brazilian and global data sources ranging from species data - species names, sy-nonyms, taxonomical classifica-tions - to literature, occurrence maps and images: Catalogue of

Life, List of Species of the Brazilian Flora, speciesLink, Bio-diversity Heritage Library, Bioline International, Global Biodiversity Information Facility (GBIF).

EUBrazilOpenBio Gateway

https://portal.eubrazilopenbio.d4science.org

EUBrazilOpenBio gateway is an access point to a number of resources (data and services including computing fa-cilities) operated by the EUBrazilOpenBio infrastructure. It serves the needs of biodiversity scientists and information specialists involved in the development and alignment of species taxonomies and in the modeling and projection of ecological niche models to predict and to understand the distribution of species. The gateway provides the user community with applica-tions enhanced with seamless access to species specimen, and complementary relevant data from multiple providers.

An Infrastructure beyond Computing and Storage Resources

EUBrazilOpenBio operates a Hybrid Data Infrastructure, i.e. a new type of Data Infrastructure specifically conceived to deal with data-intensive science. Such an infrastructure nicely integrates several technologies, infrastructures and information systems to enable a data-management-capa-bility delivery model in which computing, storage, data and software are made available by the Infrastructure as-a-Service.

Integration between Regional & Global Taxonomies

EUBrazilOpenBio developed a new version of the i4Life cross-mapping tool to compare regional and global taxonomies, such as the list of species of Brazilian Flora, containing over 43,000 species plus around 30,000 synonyms, and the global Species2000/ITIS Ca-talogue of Life (CoL), indexing about 250,000 plant species and 300,000 synonyms.

Cross-map a checklist of taxa (Checklist A) from the Flora of Brazil catalogue with another one (Checklist B) from the Species 2000 / ITIS Catalogue of Life.

Explore and analyse di-sparities between taxa in Checklists A and B, iden-tifying missing taxa from Checklist B.

Consider that: »A taxon in Checklist A may be known by a different name in Checklist B »A subset of a taxon that appears in Checklist B (or vice versa) »It overlaps partially with a taxon in Checklist B

The cross-mapping tool enables taxonomi-sts and data curators to find relationships between lists of species and higher taxa in two different species information systems. Examples of relationships are: “not_found_in”, “corresponds”, “includes”, “included_by”, and “overlaps”. This tool makes it easier for scientists to work with diverse taxonomic data from multiple sources.

Data usability and the use of ecological niche modeling

Practical problems in applying ENM are associated with intensive computational requi-rements when models need to be generated for a large number of species using com-plex modeling strategies involving several algorithms and high-resolution environmen-tal data. A new application, developed as part of EUBrazilOpenBio, allows scientists to carry out complex ecological niche modeling experiments on the Web. The application exploits aggregated computational resources available to the project, which includes the EGI Fe-derated Cloud through interoperability features of the VENUS-C COMPSs middleware. Additionally, scientists have seamless access to different specimen data networks, such as GBIF and speciesLink, which integrates data from more than 200 distributed biologi-cal collections in Brazil.

Create a model from the oc-currence points in GBIF and SpeciesLink and Worldclim maps

Test the accuracy of the model

Project the model under new environmental condi-tions

The cloud-enabled niche modeling Service developed in EUBrazilOpenBio can also ser-ve external applications, such as the Brazi-lian Virtual Herbarium and the Biodiversity Virtual eLaboratory (BioVel) project. In this case, enabling the execution of ecological niche modeling workflows using the same computational facilities.

Training resources

EUBrazilOpenBio is producing training material to guide new users to use and understand the potential of this system. The training material will explain the EUBrazilOpenBio use cases, including practical exercises and some background information. Material will also be available for training new developers that could bring new applications within the EU-BrazilOpenBio platform. All the training material will be available through the project website.