BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.

Journal: Nucleic acids research
Published Date: Jan 8, 2020

Abstract

The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, the website has allowed users to browse and search metabolic models. Within this update, we detail new content and features in the repository, continuing the original effort to connect each model to genome annotations and external databases as well as standardization of reactions and metabolites. We describe the addition of 31 new models that expand the portion of the phylogenetic tree covered by BiGG Models. We also describe new functionality for hosting multi-strain models, which have proven to be insightful in a variety of studies centered on comparisons of related strains. Finally, the models in the knowledge base have been benchmarked using Memote, a new community-developed validator for genome-scale models to demonstrate the improving quality and transparency of model content in BiGG Models.

Authors

  • Charles J Norsigian
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
  • Neha Pusarla
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
  • John Luke McConn
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
  • James T Yurkovich
    Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
  • Andreas Dräger
    Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany.
  • Bernhard O Palsson
    Department of Bioengineering, University of California, San Diego, CA, USA.
  • Zachary King
    Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.

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