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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: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: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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Works referenced in this record:

Implications of Big Data for cell biology
journal, July 2015

  • Dolinski, Kara; Troyanskaya, Olga G.
  • Molecular Biology of the Cell, Vol. 26, Issue 14
  • DOI: 10.1091/mbc.E13-12-0756

The National Institutes of Health's Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data
journal, November 2014

  • Margolis, Ronald; Derr, Leslie; Dunn, Michelle
  • Journal of the American Medical Informatics Association, Vol. 21, Issue 6
  • DOI: 10.1136/amiajnl-2014-002974

Data, information, knowledge and principle: back to metabolism in KEGG
journal, November 2013

  • Kanehisa, Minoru; Goto, Susumu; Sato, Yoko
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1076

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
journal, November 2013

  • Caspi, Ron; Altman, Tomer; Billington, Richard
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1103

Saccharomyces genome database provides new regulation data
journal, November 2013

  • Costanzo, Maria C.; Engel, Stacia R.; Wong, Edith D.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1158

The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease
journal, October 2014

  • Eppig, Janan T.; Blake, Judith A.; Bult, Carol J.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku967

Reconstruction of biochemical networks in microorganisms
journal, December 2008

  • Feist, Adam M.; Herrgård, Markus J.; Thiele, Ines
  • Nature Reviews Microbiology, Vol. 7, Issue 2
  • DOI: 10.1038/nrmicro1949

Constraint-based models predict metabolic and associated cellular functions
journal, January 2014

  • Bordbar, Aarash; Monk, Jonathan M.; King, Zachary A.
  • Nature Reviews Genetics, Vol. 15, Issue 2
  • DOI: 10.1038/nrg3643

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
journal, February 2012

  • Lewis, Nathan E.; Nagarajan, Harish; Palsson, Bernhard O.
  • Nature Reviews Microbiology, Vol. 10, Issue 4
  • DOI: 10.1038/nrmicro2737

The evolution of genome-scale models of cancer metabolism
journal, January 2013


Next-generation genome-scale models for metabolic engineering
journal, December 2015


Co-evolution of strain design methods based on flux balance and elementary mode analysis
journal, December 2015


Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli
journal, January 2013

  • McCloskey, Douglas; Palsson, Bernhard Ø; Feist, Adam M.
  • Molecular Systems Biology, Vol. 9, Issue 1
  • DOI: 10.1038/msb.2013.18

Towards multidimensional genome annotation
journal, February 2006

  • Reed, Jennifer L.; Famili, Iman; Thiele, Ines
  • Nature Reviews Genetics, Vol. 7, Issue 2
  • DOI: 10.1038/nrg1769

A protocol for generating a high-quality genome-scale metabolic reconstruction
journal, January 2010


Optimizing genome-scale network reconstructions
journal, May 2014

  • Monk, Jonathan; Nogales, Juan; Palsson, Bernhard O.
  • Nature Biotechnology, Vol. 32, Issue 5
  • DOI: 10.1038/nbt.2870

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
journal, January 2010

  • Schellenberger, Jan; Park, Junyoung O.; Conrad, Tom M.
  • BMC Bioinformatics, Vol. 11, Issue 1
  • DOI: 10.1186/1471-2105-11-213

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
journal, March 2003


MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks
journal, January 2013


HMDB 3.0—The Human Metabolome Database in 2013
journal, November 2012

  • Wishart, David S.; Jewison, Timothy; Guo, An Chi
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1065

Using Bioconductor Package BiGGR for Metabolic Flux Estimation Based on Gene Expression Changes in Brain
journal, March 2015


MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
journal, January 2012

  • Kumar, Akhil; Suthers, Patrick F.; Maranas, Costas D.
  • BMC Bioinformatics, Vol. 13, Issue 1
  • DOI: 10.1186/1471-2105-13-6

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
journal, August 2015


Improving Collaboration by Standardization Efforts in Systems Biology
journal, December 2014

  • Dräger, Andreas; Palsson, Bernhard Ø.
  • Frontiers in Bioengineering and Biotechnology, Vol. 2
  • DOI: 10.3389/fbioe.2014.00061

RefSeq: an update on mammalian reference sequences
journal, November 2013

  • Pruitt, Kim D.; Brown, Garth R.; Hiatt, Susan M.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1114

The Reactome pathway knowledgebase
journal, November 2013

  • Croft, David; Mundo, Antonio Fabregat; Haw, Robin
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1102

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
journal, November 2014

  • Rose, Peter W.; Prlić, Andreas; Bi, Chunxiao
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1214

High-throughput generation, optimization and analysis of genome-scale metabolic models
journal, August 2010

  • Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A.
  • Nature Biotechnology, Vol. 28, Issue 9
  • DOI: 10.1038/nbt.1672

Gene: a gene-centered information resource at NCBI
journal, October 2014

  • Brown, Garth R.; Hem, Vichet; Katz, Kenneth S.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1055

Computing the functional proteome: recent progress and future prospects for genome-scale models
journal, August 2015


COBRApy: COnstraints-Based Reconstruction and Analysis for Python
journal, January 2013

  • Ebrahim, Ali; Lerman, Joshua A.; Palsson, Bernhard O.
  • BMC Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1186/1752-0509-7-74

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
journal, August 2011

  • Schellenberger, Jan; Que, Richard; Fleming, Ronan M. T.
  • Nature Protocols, Vol. 6, Issue 9
  • DOI: 10.1038/nprot.2011.308

GenBank
journal, November 2014

  • Benson, Dennis A.; Clark, Karen; Karsch-Mizrachi, Ilene
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1216

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
journal, December 2011

  • Juty, N.; Le Novere, N.; Laibe, C.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1097

A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011
journal, January 2011

  • Orth, Jeffrey D.; Conrad, Tom M.; Na, Jessica
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2011.65

JSBML 1.0: providing a smorgasbord of options to encode systems biology models: Table 1.
journal, June 2015


Controlled vocabularies and semantics in systems biology
journal, January 2011

  • Courtot, Mélanie; Juty, Nick; Knüpfer, Christian
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2011.77

    Works referencing / citing this record:

    Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data
    journal, June 2019

    • Amin, Sara A.; Chavez, Elizabeth; Porokhin, Vladimir
    • Microbial Cell Factories, Vol. 18, Issue 1
    • DOI: 10.1186/s12934-019-1156-3

    Closing the gap between formats for storing layout information in systems biology
    journal, July 2019

    • Hoksza, David; Gawron, Piotr; Ostaszewski, Marek
    • Briefings in Bioinformatics
    • DOI: 10.1093/bib/bbz067

    NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
    journal, June 2019


    Current status and applications of genome-scale metabolic models
    journal, June 2019


    A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase
    journal, December 2018

    • Lieven, Christian; Petersen, Leander A. H.; Jørgensen, Sten Bay
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.02947

    A systematic assessment of current genome-scale metabolic reconstruction tools
    journal, August 2019


    Modeling Meets Metabolomics—The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans
    journal, November 2018

    • Witting, Michael; Hastings, Janna; Rodriguez, Nicolas
    • Frontiers in Molecular Biosciences, Vol. 5
    • DOI: 10.3389/fmolb.2018.00096

    Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering
    journal, June 2019

    • Landon, Sophie; Rees-Garbutt, Joshua; Marucci, Lucia
    • Essays in Biochemistry, Vol. 63, Issue 2
    • DOI: 10.1042/ebc20180045

    Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome
    journal, June 2019

    • Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel
    • eLife, Vol. 8
    • DOI: 10.7554/elife.39733

    Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks
    journal, June 2019