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COEUS: “semantic web in a box” for biomedical applications

Pedro Lopes* and José Luís Oliveira

Author Affiliations

DETI/IEETA, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, 3810 – 193, Portugal

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Journal of Biomedical Semantics 2012, 3:11  doi:10.1186/2041-1480-3-11

Published: 17 December 2012

Abstract

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/ webcite.

Keywords:
Semantic web framework; Rapid application deployment; Linked data; Web services; Biomedical applications; Biomedical semantics