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

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

Posted 01 Apr 2020
bioRxiv DOI: 10.1101/2020.03.31.018663

For over ten 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. Conclusion: This database serves as a transparent source of biochemistry data to broadly support mechanistic modeling and data integration. ### Competing Interest Statement The authors have declared no competing interest.

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