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

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

doi:10.1093/nar/gkaa1143

Key Points

To provide a centralized biochemistry database that integrates metabolic annotations to enable the reconstruction, comparison, and analysis of genome-scale metabolic models across plants, fungi, and microbes.
Aggregated and curated biochemical reactions, chemical compounds, and metabolic annotations across diverse kingdoms of life.
Maintained public computational access via a dedicated web repository interface.
Established a consistent, unified biochemical reference framework to automate and standardize metabolic network reconstructions.
Provided updated repository endpoints to ensure direct access to biochemical curation tables and modeling utilities.

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Implication

Database report presents an integrated biochemical resource for plants, fungi, and microbes, highlighting streamlined genome-scale metabolic reconstruction.

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Seaver et al. (2020) studied this question.

synapsesocial.com/papers/6ab498812a9f699624eb7cc7 https://doi.org/10.1093/nar/gkaa1143

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

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

Key Points

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