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

King, Zachary A.; Lu, Justin; Drager, Andreas; Miller, Philip; Federowicz, Stephen; Lerman, Joshua A.; Ebrahim, Ali; Palsson, Bernhard O.; Lewis, Nathan E.

doi:10.1093/nar/gkv1049

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

Journal Article · 16 October 2015 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkv1049 · OSTI ID:1253623

King, Zachary A. ^[1]; Lu, Justin ^[2];

^[3]; Miller, Philip ^[2]; Federowicz, Stephen ^[2];

^[2]; Ebrahim, Ali ^[2]; Palsson, Bernhard O. ^[2]; Lewis, Nathan E. ^[2]

Univ. of California, San Diego, La Jolla, CA (United States); University of California, San Diego
Univ. of California, San Diego, La Jolla, CA (United States)
Univ. of California, San Diego, La Jolla, CA (United States); Univ. of Tuebingen, Tubingen (Germany)

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.

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Research Organization:: Univ. of California, San Diego, La Jolla, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0008701

OSTI ID:: 1253623

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 44; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Metabolic adaptations underlying genome flexibility in prokaryotes Goyal, Akshit PLOS Genetics, Vol. 14, Issue 10 https://doi.org/10.1371/journal.pgen.1007763	journal	October 2018
biochem4j: Integrated and extensible biochemical knowledge through graph databases Swainston, Neil; Batista-Navarro, Riza; Carbonell, Pablo PLOS ONE, Vol. 12, Issue 7 https://doi.org/10.1371/journal.pone.0179130	journal	July 2017
Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3) Kim, Hanseol; Kim, Sinyeon; Yoon, Sung Ho PLOS ONE, Vol. 13, Issue 9 https://doi.org/10.1371/journal.pone.0204375	journal	September 2018
A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber Bagheri, Maryam; Marashi, Sayed-Amir; Amoozegar, Mohammad Ali PLOS ONE, Vol. 14, Issue 5 https://doi.org/10.1371/journal.pone.0216336	journal	May 2019
Reconstruction of a regulated two-cell metabolic model to study biohydrogen production in a diazotrophic cyanobacterium Anabaena variabilis ATCC 29413 Malek Shahkouhi, Ali; Motamedian, Ehsan PLOS ONE, Vol. 15, Issue 1 https://doi.org/10.1371/journal.pone.0227977	journal	January 2020
BioModelKit – An Integrative Framework for Multi-Scale Biomodel-Engineering Blätke, Mary-Ann Journal of Integrative Bioinformatics, Vol. 15, Issue 3 https://doi.org/10.1515/jib-2018-0021	journal	September 2018
Enzyme promiscuity shapes adaptation to novel growth substrates Guzmán, Gabriela I.; Sandberg, Troy E.; LaCroix, Ryan A. Molecular Systems Biology, Vol. 15, Issue 4 https://doi.org/10.15252/msb.20188462	journal	April 2019
Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans. Witting, Michael; Hastings, Janna; Rodriguez, Nicolas Frontiers Media SA https://doi.org/10.17863/cam.41386	journalarticle	January 2018
MEMOTE for standardized genome-scale metabolic model testing Lieven, Christian; Beber, Moritz E.; Olivier, Brett G. RWTH Aachen University https://doi.org/10.18154/rwth-2020-03668	text	January 2020
Horizontal Gene Transfer Drives the Evolution of Dependencies in Bacteria Goyal, Akshit SSRN Electronic Journal https://doi.org/10.2139/ssrn.3951496	journal	January 2021
Systems Medicine as an Emerging Tool for Cardiovascular Genetics Haase, Tina; Börnigen, Daniela; Müller, Christian Frontiers in Cardiovascular Medicine, Vol. 3 https://doi.org/10.3389/fcvm.2016.00027	journal	August 2016
iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE Norsigian, Charles J.; Kavvas, Erol; Seif, Yara Frontiers in Genetics, Vol. 9 https://doi.org/10.3389/fgene.2018.00121	journal	April 2018
Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G(B1) Demidenko, Aleksandr; Akberdin, Ilya R.; Allemann, Marco Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.02167	journal	January 2017
In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host Bryant, William A.; Stentz, Régis; Le Gall, Gwenaelle Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02440	journal	December 2017
A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase Lieven, Christian; Petersen, Leander A. H.; Jørgensen, Sten Bay Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02947	journal	December 2018
Modeling Meets Metabolomics—The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans Witting, Michael; Hastings, Janna; Rodriguez, Nicolas Frontiers in Molecular Biosciences, Vol. 5 https://doi.org/10.3389/fmolb.2018.00096	journal	November 2018
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR Pawar, Gopal; Madden, Judith C.; Ebbrell, David Frontiers in Pharmacology, Vol. 10 https://doi.org/10.3389/fphar.2019.00561	journal	June 2019
The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions Jacoby, Richard; Peukert, Manuela; Succurro, Antonella Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.01617	journal	September 2017
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview Sen, Partho; Orešič, Matej Metabolites, Vol. 9, Issue 2 https://doi.org/10.3390/metabo9020022	journal	January 2019
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling Pham, Nhung; van Heck, Ruben; van Dam, Jesse Metabolites, Vol. 9, Issue 2 https://doi.org/10.3390/metabo9020028	journal	February 2019
Comparison of Multi-Objective Evolutionary Algorithms to Solve the Modular Cell Design Problem for Novel Biocatalysis Garcia, Sergio; Trinh, Cong T. Processes, Vol. 7, Issue 6 https://doi.org/10.3390/pr7060361	journal	June 2019
Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection Michael, Zimmermann,; Maria, Kogadeeva,; Gayle, McEwen, ETH Zurich https://doi.org/10.3929/ethz-b-000191307	text	January 2017
Phenotypic innovation through recombination in genome-scale metabolic networks Sayed-Rzgar, Hosseini,; C., Martin, Olivier; Andreas, Wagner, Royal Society Publishing https://doi.org/10.5167/uzh-128014	interactiveresource	January 2016
Metabolomics: Basic Principles and Strategies Nalbantoglu, Sinem Molecular Medicine https://doi.org/10.5772/intechopen.88563	book	November 2019
Essential metabolism for a minimal cell Breuer, Marian; Earnest, Tyler M.; Merryman, Chuck eLife, Vol. 8 https://doi.org/10.7554/elife.36842	journal	January 2019
Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel eLife, Vol. 8 https://doi.org/10.7554/elife.39733	journal	June 2019

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