HAMBURG, Germany - A consortium of research institutions and the genomics and bioinformatics company Lion AG was granted DM 2.4 million (US$1.3 million) by the German Federal Research Ministry BMBF to set up an "electronic atlas of metabolism."
The project will develop methods to support the modeling and simulation of biochemical pathways based on genomics information. Collaborators include Lion Bioscience AG, the Center for Molecular Biology of Heidelberg University (ZMBH), the European Molecular Biology Laboratory (EMBL), and the European Media Laboratory (EML), all based in Heidelberg.
The development of the atlas, named ELSA (Elektronischer Stoffwechsel-Atlas), will be coordinated by the Bioinformatics and Scientific Databases and Visualization groups of the EML, a private research institute dedicated to interdisciplinary research to develop novel methods of computing in cooperation with universities and industry.
EML was established in 1997 by Klaus Tschira, chairman of the Klaus Tschira Foundation, and one of the founders of the German software company SAP AG. Since December 1998 Tschira has been a member of the board of directors of Lion AG.
"The comparative analysis of genomes and protein sequences derived from sequencing projects will play an essential role in the setup of the electronic atlas," Erich Bornberg-Bauer, project manager of the EML Bioinformatics Group, told BioWorld International. "In addition, we will integrate heterogeneous data from existing databases, experimental data and computational modeling of pathways."
The atlas should help to speed up the functional analysis of newly sequenced genes through gene comparison, he added. "Ideally, we aim at the automated reconstruction of all biochemical pathways of an organism, given only its genomic sequence."
Already, the EML's Bioinformatics group is working in close cooperation with ZMBH to create an integrated database for the computational analysis and visualization of biochemical pathways based on the analysis of Mycoplasma pneumonia, a model organism sequenced by ZMBH. This organism is one of the smallest free-living cells, with only a few hundred genes. Therefore it can be used as a model to study the minimal gene set necessary for a minimal metabolism.
Ninety percent of the coding regions already have been identified, and 50 percent of all genes show significant sequence homology to defined genes with known function from other bacteria.
To construct a complete representation of the metabolic pathways, information about locations, sequences, structures, domains and associated functions will be mapped onto the topology of the biochemical data model. In a next step, data from other microbial organisms will be added. In the end, users of the database will gain suggestions about the possible function of newly sequenced genes or proteins. To complete the atlas, Lion AG will retrieve and integrate data from heterogeneous data sources.
"To us, ELSA will be an additional module to our bioinformatics platform," Claus Kremoser, director of strategy and business development of Lion AG, told BioWorld International. "It will provide an intelligent visualization of the metabolism with many links to databases, data from DNA arrays, protein sequences, etc."
EMBL, the fourth cooperation partner, will contribute methods to predict the function of genes and proteins by sequence comparison.