Bio2X: a rule-based approach for semi-automatic transformation of semi-structured biological data to XML

Authors:
Song Yang;Sourav S. Bhowmick;Sanjay Madria
Affiliations:
School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore;School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore;Department of Computer Science, University of Missouri-Rolla, Rolla
Venue:
Data & Knowledge Engineering - Special issue: XML schema and data management
Year:
2005

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Abstract

Data integration of geographically dispersed, heterogeneous, complex biological databases is a key research area. One of the key features of a successful data integration system is to have a simple self-describing data exchange format. However, many of the biological databases provide data in flat files which are poor data exchange formats. Fortunately, XML can be viewed as a powerful data model and better data exchange format. In this paper, we present the Bio2X system that transforms flat file data into highly hierarchical XML data using rule-based machine learning technique. Bio2X has been fully implemented using Java. Our experiments to transform real world biological data demonstrate the effectiveness of the Bio2X approach.