This article appears in the following Briefings in Bioinformatics issue: Special Issue:Database Integration in Life Sciences [View the issue table of contents]
Solutions for data integration in functional genomics: a critical assessment and case study
Corresponding author. Damian Smedley, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. Tel: +44-1223-494451; Fax: +44-1223-494468; E-mail: damian{at}ebi.ac.uk
The torrent of data emerging from the application of new technologies to functional genomics and systems biology can no longer be contained within the traditional modes of data sharing and publication with the consequence that data is being deposited in, distributed across and disseminated through an increasing number of databases. The resulting fragmentation poses serious problems for the model organism community which increasingly rely on data mining and computational approaches that require gathering of data from a range of sources. In the light of these problems, the European Commission has funded a coordination action, CASIMIR (coordination and sustainability of international mouse informatics resources), with a remit to assess the technical and social aspects of database interoperability that currently prevent the full realization of the potential of data integration in mouse functional genomics. In this article, we assess the current problems with interoperability, with particular reference to mouse functional genomics, and critically review the technologies that can be deployed to overcome them. We describe a typical use-case where an investigator wishes to gather data on variation, genomic context and metabolic pathway involvement for genes discovered in a genome-wide screen. We go on to develop an automated approach involving an in silico experimental workflow tool, Taverna, using web services, BioMart and MOLGENIS technologies for data retrieval. Finally, we focus on the current impediments to adopting such an approach in a wider context, and strategies to overcome them.
Keywords: data integration, interoperability, web services, BioMart, MOLGENIS, Taverna
*These authors contributed equally to this work.
The authors are bioinformaticians working together as part of the CASIMIR project, which aims to develop policy and principles to underpin the development of data integration in the biosciences.
Submitted: July 2, 2008. Received (in revised form): September 8, 2008.
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