The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Seaver, Samuel M. D.; Liu, Filipe; Zhang, Qizhi; Jeffryes, James; Faria, José P.; Edirisinghe, Janaka N.; Mundy, Michael; Chia, Nicholas; Noor, Elad; Beber, Moritz E.; Best, Aaron A.; DeJongh, Matthew; Kimbrel, Jeffrey A.; D’haeseleer, Patrik; McCorkle, Sean R.; Bolton, Jay R.; Pearson, Erik; Canon, Shane; Wood-Charlson, Elisha M.; Cottingham, Robert W.; Arkin, Adam P.; Henry, Christopher S.

doi:10.1093/nar/gkaa746

Title: The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Journal Article · 28 September 2020 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkaa746 · OSTI ID:1668123

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Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
Department of Biology, Hope College, Holland, MI 49423, USA
Department of Computer Science, Hope College, Holland, MI 49423, USA
Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA

Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.

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Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-06CH11357; AC02-05CH11231; AC05-00OR22725; AC52-07NA27344

OSTI ID:: 1668123

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 49; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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