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Lopes-2012e

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Article

Title COEUS: “semantic web in a box” for biomedical applications
Author Pedro Lopes, José Luís Oliveira
Journal Journal of Biomedical Semantics
Volume 3
Number 11
Pages
Month December
Year 2012
DOI 10.1186/2041-1480-3-11
Group Biomedical Informatics and Technologies
Group (before 2015) Transverse Activity on Innovative Biomedical Technologies, Information Systems and Telematics Laboratory
Indexed by ISI Yes

Background: As the omics revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter?s complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited.

Results: COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a ?semantic web in a box? approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer.

Conclusions: The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/.