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Bioinformatics

Unified access to bioinformatic resources: SRS, Biomart and EB-Eye

Programmatic access to data and tools through the Web using so-called Web services has an important role in bioinformatics. In this poster we present an overview of three commonly used search and retrieval systems for biological information: EB-Eye, Biomart and SRS and present a web service built over WS-I and REST technologies that provides an integration layer and a common interface to them. We will also present an AJAX search application built on top of these webservices.
As new technological developments in biological research have allowed the collection of larger and more diverse data types, major players in the bioinformatics field have endeavored to stay at the forefront of this research, providing new and increasingly sophisticated resources to access the data. There are a different open source and commercial systems that have been developed as a solution to the data integration challenge, for example, SRS [1],[2], BioMart [3] and the EB-Eye [4]. These tools are mainly accessed using browser-based interfaces, however, Web Services technology has gained much attention as an open architecture enabling interoperability among applications across heterogeneous platforms and different networks, and they also offer either REST or SOAP interfaces, that allow bioinformaticians to access the data programmatically.
The aim of this work is to present an overview of these interfaces, and suggest a common API that provides a unique access point to the three interfaces. On top of this API, we have developed a web service that integrates the best mechanism of the different services: the SOAP interface of EB-Eye, the URL query language of SRS and the XML query syntax of Biomart, so we can interact with the three systems in the same way.
[1] http://srs.ebi.ac.uk/
[2] http://srs.embl.de
[3] http://www.ebi.ac.uk/biomart
[4] http://www.ebi.ac.uk/ebisearch/advancedsearch.ebi
Keywords: EBI, SRS, Biomart, SOAP, REST, web services

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