Challenges to be faced in the reconstruction of metabolic networks from public databases.
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.
Poolman
M G
MG
School of Biology and Molecular Science, Oxford Brookes University, Oxford OX3 0BP, UK. mgpoolman@brookes.ac.uk
Bonde
B K
BK
Gevorgyan
A
A
Patel
H H
HH
Fell
D A
DA
D000465:Algorithms; D000818:Animals; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D003628:Database Management Systems; D016208:Databases, Factual; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D007700:Kinetics; D008954:Models, Biological; D009097:Multienzyme Complexes / Q000378:metabolism*; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D014584:User-Computer Interface
D009097:Multienzyme Complexes; D020543:Proteome