Bioinformatics pathway representations, databases, and algorithms
Part 4. Bioinformatics
4.7. Structuring and Integrating Data
Short Specialist Review
Published Online: 15 APR 2005
Copyright © 2005 John Wiley & Sons, Ltd
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
How to Cite
Karp, P. D. 2005. Bioinformatics pathway representations, databases, and algorithms. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.7:88.
- Published Online: 15 APR 2005
Management of pathway information is of great importance in bioinformatics because pathways place gene products in a causal, mechanistic context showing how those gene products contribute to a larger biological process, and allow us to reason about perturbations to a living system. In the postgenomic era, pathways are also an important organizational and information-reduction device that decreases the cognitive complexity of a biological system by allowing us to reason about a system at the level of pathways instead of at the level of proteins.
Management of pathway data is a challenging area of bioinformatics because it involves a host of representational and algorithmic problems. This article explores pathway representations and reviews existing pathway databases. It also presents a number of algorithms for computing with pathways, including algorithms for pathway prediction, algorithms for predicting which genes code for missing enzymes in metabolic pathways, algorithms for flux-balance analysis, and algorithms for qualitatively propagating metabolites through a metabolic network.
- Metabolic pathways;
- pathway bioinformatics;
- pathway prediction;
- pathway representation;
- pathway databases;
- flux-balance analysis