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

By Zachary A. King, Justin Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A. Lerman, Ali Ebrahim, Bernhard O. Palsson, Nathan E. Lewis. Nucleic Acids Res., 2015

886 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f148264f42c5119182ac9152f9225bdfbccfbc34

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Citations in the corpus

Epistasis and Adaptation on Fitness Landscapes (2022, background): “Taking this to the organismal level, systems biologists have developed complex genome-scale metabolic models that predict phenotypes across environments (King et al. 2016, Bordbar et al. 2014).”
BioModels—15 years of sharing computational models in life science (2019, background): “At the COMBINE (http://co.mbine.org/) 2019 meeting (http://co.mbine.org/events/COMBINE 2019), we have initiated community discussion to jointly develop ModeleX-change, a lightweight, metadata-based infrastructure for the collaborative discovery of systems biology models and model components across i”
Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism (2018, positive): “We added reactions from HMR 2.0 21 (2,478), a drug module 22 (721), a transport module 23 (51), host-microbe reactions 10 (24), and absorption and metabolism of dietary compounds (20).”
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities (2018, methodology): “A comparison between the reaction contents of BiGG, modelSEED and KEGG (Supplementary Figure S6), shows that BiGG contains a large number of reactions which are not present in the other databases (most likely a consequence of the manual curation efforts), but lags behind in terms of total coverage o”
The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions (2017, background): “The simplest division, typically for prokaryotic organisms, is between an external and an internal (cytosolic) compartment, while plant GEMs will have compartments for different tissues as well.”
Review on natural products databases: where to find data in 2020 (2020, neutral): “King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA et al (2016) BiGG Models: a platform for integrating, standardizing and sharing genome-scale models.”
The RCSB protein data bank: integrative view of protein, gene and 3D structural information (2016, methodology): “Reconstructions of pathways are based on the BiGG Models (25), a knowledgebase of biochemically, genetically and genomically structured genome-scale metabolic network reconstructions.”