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Bioinformatics pathway representations, databases, and algorithms

Part 4. Bioinformatics

4.7. Structuring and Integrating Data

Short Specialist Review

  1. Peter D. Karp

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g408308

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

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.

Author Information

  1. Bioinformatics Research Group, Menlo Park, CA, USA

Publication History

  1. Published Online: 15 APR 2005

Abstract

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.

Keywords:

  • Metabolic pathways;
  • pathway bioinformatics;
  • pathway prediction;
  • pathway representation;
  • pathway databases;
  • flux-balance analysis