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ready ModelSEED Biochemistry Database

General Information
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. The ModelSEED biochemistry database is the foundation of the biochemical data underlying ModelSEED and KBase. The The ModelSEED biochemistry database (i) includes compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) is extensible by the user community, with all data stored in GitHub; and (iii) designed 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.

How to cite this record ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI:; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Dec 08 2021 10:06 a.m.

This record is maintained by seaver

Record added: Oct. 15, 2020, 9:07 p.m.
Record updated: Feb. 4, 2021, 1:23 p.m. by The FAIRsharing Team.

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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

Samuel M D Seaver, Filipe Liu, Qizhi Zhang et al.
Nucleic Acids Research 2020

View Paper (PubMed) View Publication

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  • This record is maintained by seaver




Grant Number(s)

  • 686070 (DD-DeCaF) (European Union's Horizon 2020 research and innovation programme)

  • DE-AC02–05CH11231 (United States Department of Energy, Office of Science, USA)

  • DE-AC02–06CH11357 (United States Department of Energy, Office of Science, USA)

  • DE-AC05–00OR22725 (United States Department of Energy, Office of Science, USA)

  • DE-AC52–07NA27344 (United States Department of Energy, Office of Science, USA)

  • GEPR-1444202 (National Science Foundation (NSF), USA)

  • MCB-1716285 (National Science Foundation (NSF), USA)

  • R01CA179243 (National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, USA)