Challenges to be faced in the reconstruction of metabolic networks from public databases

Syst Biol (Stevenage). 2006 Sep;153(5):379-84. doi: 10.1049/ip-syb:20060012.

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.

MeSH terms

  • Algorithms
  • Animals
  • Cell Physiological Phenomena*
  • Computer Simulation
  • Database Management Systems
  • Databases, Factual*
  • Humans
  • Information Storage and Retrieval / methods*
  • Kinetics
  • Models, Biological*
  • Multienzyme Complexes / metabolism*
  • Proteome / metabolism*
  • Signal Transduction / physiology*
  • User-Computer Interface

Substances

  • Multienzyme Complexes
  • Proteome