Challenges to be faced in the reconstruction of metabolic networks from public databases |
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Authors: | Poolman M G Bonde B K Gevorgyan A Patel H H Fell D A |
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Affiliation: | School of Biology and Molecular Science, Oxford Brookes University, Oxford OX3 0BP, UK. mgpoolman@brookes.ac.uk |
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Abstract: | In the post-genomic era, the biochemical information for individual compounds, enzymes, reactions to be found within named organisms has become readily available. The well-known KEGG and BioCyc databases provide a comprehensive catalogue for this information and have thereby substantially aided the scientific community. Using these databases, the complement of enzymes present in a given organism can be determined and, in principle, used to reconstruct the metabolic network. However, such reconstructed networks contain numerous properties contradicting biological expectation. The metabolic networks for a number of organisms are reconstructed from KEGG and BioCyc databases, and features of these networks are related to properties of their originating database. |
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