Building in-silico pathway SBML models from heterogeneous sources

Abstract

The recent revolutionary developments concerning the high throughput (-omics) measuring techniques in life sciences is expediting the way for the development of in silico models envisioning the Systems biology perspective in the description of biological problems. As a resuit, very large open biological databases provide in silico descriptions in various formats, of biochemical pathways related to various cellular physiological aspects across the evolutionary climax. However, the lack of standardization regarding conceptual biological data representation incurs sheer limitations with respect to the functionality as well as the scientific completeness of the respective models. In this work, a software solution is presented which successfully bridges the gap towards building in-silico metabolic pathway models in Systems Biology Markup Language (SBML) format (standard SBML, CellDesigner SBML) by exploiting various XML based formats (SBML, KGML- KEGG Markup Language-, CellML - Cell Markup Language-, for pathway representation). Our solution provides methods for the biochemically correct transformation, curation and automatic simulation of the pathways, thus accomplishing the setup of fully functional in-silico models.