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

Karp, Peter; Ouzounis, Christos; Moore-Kochlacs, Caroline; Goldovsky, Leon; Kaipa, Pallavi; Ahrén, Dag LU ; Tsoka, Sophia; Darzentas, Nikos; Kunin, Victor and López-Bigas, Núria (2005) In Nucleic Acids Research 33(19). p.6083-6089
Abstract
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... (More)
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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Nucleic Acids Research
volume
33
issue
19
pages
6083 - 6089
publisher
Oxford University Press
external identifiers
  • scopus:27244436714
ISSN
1362-4962
DOI
10.1093/nar/gki892
language
English
LU publication?
no
id
6b1bb17a-1025-403c-8252-49287931f14a (old id 952399)
date added to LUP
2008-01-31 16:06:47
date last changed
2017-11-19 03:30:19
@article{6b1bb17a-1025-403c-8252-49287931f14a,
  abstract     = {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.},
  author       = {Karp, Peter and Ouzounis, Christos and Moore-Kochlacs, Caroline and Goldovsky, Leon and Kaipa, Pallavi and Ahrén, Dag and Tsoka, Sophia and Darzentas, Nikos and Kunin, Victor and López-Bigas, Núria},
  issn         = {1362-4962},
  language     = {eng},
  number       = {19},
  pages        = {6083--6089},
  publisher    = {Oxford University Press},
  series       = {Nucleic Acids Research},
  title        = {Expansion of the BioCyc collection of pathway/genome databases to 160 genomes},
  url          = {http://dx.doi.org/10.1093/nar/gki892},
  volume       = {33},
  year         = {2005},
}