Bioinformatics and data integration - an XML approach

Abstract

The extensible markup language (XML), which has emerged as a standard for structuring documents, notably for World Wide Web is of great interest to the bioinformatics research community. Biological sequences that are stored in different databanks require standard software computational tools for sequence identifications, structural analysis and visualization. Recently bioinformatics applications make use of XML technology due to its flexibility, durability, data modeling capability, data interoperability and open framework possibility for defining standards. The traditional architectures available in literature are lagging in terms of standard formats for biological data integration. This work describes the features and limitations of those architectures and investigates the need for a remodeled architecture in terms of using technologies such as extensible style sheet languages (XSL), XSL translators (XSLT), document object model (DOM) and application program interface (API). The proposed architecture is intended to extract and handle the biological data from the different databanks.