Vertical integration of bioinformatics tools and information processing on analysis outcome

Authors:
Andigoni Malousi;Vassilis Koutkias;Ioanna Chouvarda;Nicos Maglaveras
Affiliations:
Lab. of Medical Informatics, Faculty of Medicine, Aristotle University, Thessaloniki, Greece;Lab. of Medical Informatics, Faculty of Medicine, Aristotle University, Thessaloniki, Greece;Lab. of Medical Informatics, Faculty of Medicine, Aristotle University, Thessaloniki, Greece;Lab. of Medical Informatics, Faculty of Medicine, Aristotle University, Thessaloniki, Greece
Venue:
ISBMDA'05 Proceedings of the 6th International conference on Biological and Medical Data Analysis
Year:
2005

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Abstract

Biological sources integration has been addressed in several frameworks, considering both information sources incompatibilities and data representation heterogeneities. Most of these frameworks are mainly focused on coping with interoperability constraints among distributed databases that contain diverse types of biological data. In this paper, we propose an XML-based architecture that extends integration efforts from the distributed data sources domain to heterogeneous Bioinformatics tools of similar functionalities (“vertical integration”). The proposed architecture is based on the mediator/wrapper integration paradigm and a set of prescribed definitions that associates the capabilities and functional constraints of each analysis tool. The resulting XML-formatted information is further exploited by a visualization module that generates comparative views of the analysis outcome and a query mechanism that handles multiple information sources. The applicability of the proposed integration architecture and the information handling mechanisms was tested and substantiated on widely-known ab-initio gene finders that are publicly accessible through Web interfaces.