Bioinformatics service reconciliation by heterogeneous schema transformation

Authors:
Lucas Zamboulis;Nigel Martin;Alexandra Poulovassilis
Affiliations:
School of Computer Science and Information Systems, Birkbeck, Univ. of London and Department of Biochemistry and Molecular Biology, University College London;School of Computer Science and Information Systems, Birkbeck, Univ. of London;School of Computer Science and Information Systems, Birkbeck, Univ. of London
Venue:
DILS'07 Proceedings of the 4th international conference on Data integration in the life sciences
Year:
2007

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Abstract

This paper focuses on the problem of bioinformatics service reconciliation in a generic and scalable manner so as to enhance interoperability in a highly evolving field. Using XML as a common representation format, but also supporting existing flat-file representation formats, we propose an approach for the scalable semi-automatic reconciliation of services, possibly invoked from within a scientific workflows tool. Service reconciliation may use the AutoMed heterogeneous data integration system as an intermediary service, or may use AutoMed to produce services that mediate between services. We discuss the application of our approach for the reconciliation of services in an example bioinformatics workflow. The main contribution of this research is an architecture for the scalable reconciliation of bioinformatics services.