About BiGG Models

BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions.

BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). For details about updates to the BiGG Models website and database, see the updates page and the GitHub repository.

BiGG is freely available for non-commercial use. It is hosted and maintained by the Systems Biology Research Group at the University of California, San Diego.

BiGG Models has replaced the original BiGG Database. If you are looking for the old BiGG, you can still find it here:

http://bigg1.ucsd.edu

If you have questions or find any bugs in the database, please sumbit an issue to our issue tracker or contact Zachary King (zaking-AT-ucsd-DOT-edu).

How do I use BiGG Models?

BiGG can be browsed on this website or accessed using a web API. Try searching for a metabolite, reaction, gene, or organism in the search box to browse the content of genome-scale models. Question marks like this ? are available throughout the site to provide more help. Further information is available in the BiGG Models publication.

How do I add my model to BiGG?

We encourage contributions of models to BiGG. The following are the minimal requirements for acceptance into the knowledge base:

  • A genome-scale metabolic network reconstruction that has been published in a peer-reviewed journal
  • A COBRApy-compatible file (SBML, MAT, or JSON) representing all model content, ideally included as a supplementary file to the original publication
  • The accession ID for a NCBI RefSeq genome annotation. In some cases we can accept genome annotations in Genbank format, but we prefer annotations from a well-known genome repository.
  • Reactions, metabolites, and compartments using the BiGG Models namespace
  • Gene identifiers that match locus tags from the genome annotation

If you have all of these, please open a new issue here where the BiGG team can provide communication and feedback: https://github.com/SBRG/bigg_models/issues/new

Please note that loading models into BiGG is time-consuming, so we cannot make any guarantee regarding the time it will take to load a model.

How do I cite BiGG Models?

When using the BiGG Models knowledgebase in your research, we kindly ask that you cite the latest publication. Your citation of BiGG Models will help us to apply for ongoing funding to maintain this resource.

Latest BiGG Models publication:

King ZA, Lu JS, Dräger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and Lewis NE. BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models (2016) Nucleic Acids Research 44(D1):D515-D522. doi:10.1093/nar/gkv1049

Copyright © 2019 The Regents of the University of California

All Rights Reserved

Permission to use, copy, modify and distribute any part of BiGG Models for educational, research and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies.

Those desiring to incorporate BiGG Models into commercial products or use for commercial purposes should contact the Technology Transfer & Intellectual Property Services, University of California, San Diego, 9500 Gilman Drive, Mail Code 0910, La Jolla, CA 92093-0910, Ph: (858) 534-5815, FAX: (858) 534-7345, e-mail: [email protected].

In no event shall the University of California be liable to any party for direct, indirect, special, incidental, or consequential damages, including lost profits, arising out of the use of this bigg database, even if the University of California has been advised of the possibility of such damage.

The BiGG Models provided herein is on an "as is" basis, and the University of California has no obligation to provide maintenance, support, updates, enhancements, or modifications. The University of California makes no representations and extends no warranties of any kind, either implied or express, including, but not limited to, the implied warranties of merchantability or fitness for a particular purpose, or that the use of the BiGG Models will not infringe any patent, trademark or other rights.