A method for semi-automatic standard integration in systems biology

Abstract

The development of standards for biological pathways has led to a huge amount of model data stored in a variety of different formats represented in XML (e.g. SBML) or OWL (e.g. BioPAX). There is an urgent need for the conversion of data between the formats, but the fact that the transformation is hard to realize hampers the integration of data in the area. This article proposes a general, semi-automatic solution by transforming XML Schema based data into an OWL format. Biologists will be supported in querying data of any format and comparing different data files or schemas to each other using OWL as a common format for matching. Additionally, a backwards transformation to XML Schema is provided. The paper presents a first architectural approach and its prototype implementation. The evaluation showed that the approach is promising. © 2008 Springer-Verlag Berlin Heidelberg.