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PMID: 20426874 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.

BMC bioinformatics ·Vol. 11 ·2010-04-29 ·Pages 213

Schellenberger J, Park JO, Conrad TM, Palsson BØ

Abstract

Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabilities of organisms and interpreting experimental data. As the number of such reconstructions and analysis methods increases, there is a greater need for data uniformity and ease of distribution and use. We describe BiGG, a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest. BiGG addresses a need in the systems biology community to have access to high quality curated metabolic models and reconstructions. It is freely available for academic use at http://bigg.ucsd.edu.

MeSH Terms
Genome Genomics/methods Knowledge Bases Metabolic Networks and Pathways Software
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Schellenberger Jan
Bioinformatics Program, University of California San Diego, La Jolla, California, 92093-0419, USA.
Park Junyoung O
Conrad Tom M
Palsson Bernhard Ø
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Article Info
Journal
BMC bioinformatics
Abbr.
BMC Bioinformatics
ISSN
1471-2105
DOI
10.1186/1471-2105-11-213
Published
2010-04-29
Epub
2010-00-29
Pages
213
Language
English
Region
England
NLM ID
100965194
PMCID
PMC2874806
Subset
IM
Grants
NIGMS NIH HHS · GM00806-06 · United States
External Links
PubMed source DOI: 10.1186/1471-2105-11-213 PMC Full Text View journal details
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