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Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

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Author

  • Peter Karp
  • Christos Ouzounis
  • Caroline Moore-Kochlacs
  • Leon Goldovsky
  • Pallavi Kaipa
  • Dag Ahrén
  • Sophia Tsoka
  • Nikos Darzentas
  • Victor Kunin
  • Núria López-Bigas

Summary, in English

The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. Each PGDB in the BioCyc collection describes the genome and predicted metabolic network of a single organism, inferred from the MetaCyc database, which is a reference source on metabolic pathways from multiple organisms. In addition, each bacterial PGDB includes predicted operons for the corresponding species. The BioCyc collection provides a unique resource for computational systems biology, namely global and comparative analyses of genomes and metabolic networks, and a supplement to the BioCyc resource of curated PGDBs. The Omics viewer available through the BioCyc website allows scientists to visualize combinations of gene expression, proteomics and metabolomics data on the metabolic maps of these organisms. This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways present in these organisms, and the most frequently observed pathways. We seek scientists to adopt and curate individual PGDBs within the BioCyc collection. Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing.

Department/s

Publishing year

2005

Language

English

Pages

6083-6089

Publication/Series

Nucleic Acids Research

Volume

33

Issue

19

Document type

Journal article

Publisher

Oxford University Press

Topic

  • Biological Sciences

Status

Published

Research group

  • Microbial Ecology

ISBN/ISSN/Other

  • ISSN: 1362-4962