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Title: BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

Abstract

In this study, genome-scale metabolic models are mathematically structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.

Authors:
 [1];  [1]; ORCiD logo [2];  [1];  [1]; ORCiD logo [1];  [1];  [1];  [1]
  1. Univ. of California, San Diego, La Jolla, CA (United States)
  2. Univ. of California, San Diego, La Jolla, CA (United States); Univ. of Tuebingen, Tubingen (Germany)
Publication Date:
Research Org.:
Univ. of California, San Diego, La Jolla, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1253623
Grant/Contract Number:  
SC0008701
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 44; Journal Issue: D1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

King, Zachary A., Lu, Justin, Drager, Andreas, Miller, Philip, Federowicz, Stephen, Lerman, Joshua A., Ebrahim, Ali, Palsson, Bernhard O., and Lewis, Nathan E. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. United States: N. p., 2015. Web. doi:10.1093/nar/gkv1049.
King, Zachary A., Lu, Justin, Drager, Andreas, Miller, Philip, Federowicz, Stephen, Lerman, Joshua A., Ebrahim, Ali, Palsson, Bernhard O., & Lewis, Nathan E. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. United States. doi:https://doi.org/10.1093/nar/gkv1049
King, Zachary A., Lu, Justin, Drager, Andreas, Miller, Philip, Federowicz, Stephen, Lerman, Joshua A., Ebrahim, Ali, Palsson, Bernhard O., and Lewis, Nathan E. Sat . "BiGG Models: A platform for integrating, standardizing and sharing genome-scale models". United States. doi:https://doi.org/10.1093/nar/gkv1049. https://www.osti.gov/servlets/purl/1253623.
@article{osti_1253623,
title = {BiGG Models: A platform for integrating, standardizing and sharing genome-scale models},
author = {King, Zachary A. and Lu, Justin and Drager, Andreas and Miller, Philip and Federowicz, Stephen and Lerman, Joshua A. and Ebrahim, Ali and Palsson, Bernhard O. and Lewis, Nathan E.},
abstractNote = {In this study, genome-scale metabolic models are mathematically structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.},
doi = {10.1093/nar/gkv1049},
journal = {Nucleic Acids Research},
number = D1,
volume = 44,
place = {United States},
year = {2015},
month = {10}
}

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