By Emma Tonkin, UKOLN. In: Emerging technologies for learning. Vol. 3 (2008), p. 73-90. Research report, March 2008. © Becta 2008.

BACKGROUND: The recent availability of high-throughput data in molecular biology has increased the need for a formal representation of this knowledge domain. New ontologies are being developed to formalize knowledge, e.g. about the functions of proteins. As the Semantic Web is being introduced into the Life Sciences, the basis for a distributed knowledge-base that can foster biological data analysis is laid. However, there still is a dichotomy, in tools and methodologies, between the use of ontologies in biological investigation, that is, in relation to experimental observations, and their use as a knowledge-base. RESULTS: RDFScape is a plugin that has been developed to extend a software oriented to biological analysis with support for reasoning on ontologies in the semantic web framework. We show with this plugin how the use of ontological knowledge in biological analysis can be extended through the use of inference. In particular, we present two examples relative to ontologies representing biological pathways: we demonstrate how these can be abstracted and visualized as interaction networks, and how reasoning on causal dependencies within elements of pathways can be implemented. CONCLUSIONS: The use of ontologies for the interpretation of high-throughput biological data can be improved through the use of inference. This allows the use of ontologies not only as annotations, but as a knowledge-base from which new information relevant for specific analysis can be derived.

HCLS case study on data integration

Network Tools and Applications in Biology (NETTAB) [1] is a series of workshops focused on the most promising and innovative Information and Communication Technologies (ICT) tools and to their usefulness in Bioinformatics. These workshops aim at introducing participants to innovative network standards and technologies that are being applied to the biology field. To this end, each year a special emphasis is given to a focus theme. Workshops also include special sessions devoted both to the general theme of the series of workshops, i.e. “Network Tools and Applications in Biology”, and to further topics selected by local organizers. Biological data integration issues were already discussed in previous editions of this series of workshops, including topics such as “CORBA and XML: towards a bioinformatics integrated network environment” (NETTAB 2001) [2], “Agents in Bioinformatics” (NETTAB 2002) [3], “Workflows management: new abilities for the biological information overflow” (NETTAB 2005) [4] and “Distributed Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics” (NETTAB 2006) [5,6]. The Seventh NETTAB workshop was held at the Computer Science Department of the University of Pisa, on June 12-15, 2007, having “A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications” as focus theme. Adjunct themes were “Algorithms in bioinformatics” and “Formal Methods for Systems Biology”. This BMC Bioinformatics Supplement includes the best papers and posters – representing all the themes - from works presented at the workshop.

semantic search of pubmed using GO, FMA, and MeSH