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

BACKGROUND: 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 increase...

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Detalles Bibliográficos
Autores principales: Schellenberger, Jan, Park, Junyoung O, Conrad, Tom M, Palsson, Bernhard Ø
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874806/
https://www.ncbi.nlm.nih.gov/pubmed/20426874
http://dx.doi.org/10.1186/1471-2105-11-213
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author Schellenberger, Jan
Park, Junyoung O
Conrad, Tom M
Palsson, Bernhard Ø
author_facet Schellenberger, Jan
Park, Junyoung O
Conrad, Tom M
Palsson, Bernhard Ø
author_sort Schellenberger, Jan
collection PubMed
description BACKGROUND: 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. DESCRIPTION: 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. CONCLUSIONS: 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.
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spelling pubmed-28748062010-05-24 BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions Schellenberger, Jan Park, Junyoung O Conrad, Tom M Palsson, Bernhard Ø BMC Bioinformatics Database BACKGROUND: 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. DESCRIPTION: 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. CONCLUSIONS: 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. BioMed Central 2010-04-29 /pmc/articles/PMC2874806/ /pubmed/20426874 http://dx.doi.org/10.1186/1471-2105-11-213 Text en Copyright ©2010 Schellenberger et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database
Schellenberger, Jan
Park, Junyoung O
Conrad, Tom M
Palsson, Bernhard Ø
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
title BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
title_full BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
title_fullStr BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
title_full_unstemmed BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
title_short BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
title_sort bigg: a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874806/
https://www.ncbi.nlm.nih.gov/pubmed/20426874
http://dx.doi.org/10.1186/1471-2105-11-213
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