Novel Developments of the MetaCrop Information System for Facilitating Systems Biological Approaches

Klaus Hippe 1 , Christian Colmsee 1 , Tobias Czauderna 1 , Eva Grafahrend-Belau 1 , Björn H. Junker 1 , Christian Klukas 1 , Uwe Scholz 1 , Falk Schreiber 2 , 3  and Stephan Weise 1
  • 1 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Gatersleben, Germany
  • 2 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Gatersleben Germany
  • 3 Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle, Germany

Summary

Crop plants play a major role in human and animal nutrition and increasingly contribute to chemical or pharmaceutical industry and renewable resources. In order to achieve important goals, such as the improvement of growth or yield, it is indispensable to understand biological processes on a detailed level. Therefore, the well-structured management of fine-grained information about metabolic pathways is of high interest. Thus, we developed the MetaCrop information system, a manually curated repository of high quality information concerning the metabolism of crop plants. However, the data access to and flexible export of information of MetaCrop in standard exchange formats had to be improved. To automate and accelerate the data access we designed a set of web services to be integrated into external software. These web services have already been used by an add-on for the visualisation toolkit VANTED. Furthermore, we developed an export feature for the MetaCrop web interface, thus enabling the user to compose individual metabolic models using SBML.

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Journal + Issues

The Journal of Integrative Bioinformatics is an international journal dedicated to methods and tools of computer science and electronic infrastructure applied to biotechnology. The journal covers mainly but not exclusively data/method integration, modeling, simulation and visualization in combination with applications of theoretical/computational tools and any other approach supporting an integrative view of complex biological systems.

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