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

Autor:	Seaver SMD; Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA., Liu F; Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA., Zhang Q; Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA., Jeffryes J; Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA., Faria JP; Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA., Edirisinghe JN; Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA., Mundy M; Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA., Chia N; Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA., Noor E; Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland., Beber ME; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark., Best AA; Department of Biology, Hope College, Holland, MI 49423, USA., DeJongh M; Department of Computer Science, Hope College, Holland, MI 49423, USA., Kimbrel JA; Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA., D'haeseleer P; Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA., McCorkle SR; Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA., Bolton JR; Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Pearson E; Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Canon S; Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Wood-Charlson EM; Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Cottingham RW; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA., Arkin AP; Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Henry CS; Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2021 Jan 08; Vol. 49 (D1), pp. D575-D588.
DOI:	10.1093/nar/gkaa746
Abstrakt:	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/biochem and KBase. (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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