TY - JOUR
T1 - The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
AU - Seaver, Samuel M.D.
AU - Liu, Filipe
AU - Zhang, Qizhi
AU - Jeffryes, James
AU - Faria, José P.
AU - Edirisinghe, Janaka N.
AU - Mundy, Michael
AU - Chia, Nicholas
AU - Noor, Elad
AU - Beber, Moritz E.
AU - Best, Aaron A.
AU - DeJongh, Matthew
AU - Kimbrel, Jeffrey A.
AU - D'haeseleer, Patrik
AU - McCorkle, Sean R.
AU - Bolton, Jay R.
AU - Pearson, Erik
AU - Canon, Shane
AU - Wood-Charlson, Elisha M.
AU - Cottingham, Robert W.
AU - Arkin, Adam P.
AU - Henry, Christopher S.
N1 - Funding Information:
U.S. Department of Energy [DE-AC02-06CH11357, DEAC02-05CH11231, DE-AC05-00OR22725 to C.S.H., S.S., J.P.F., J.J., J.E., Q.Z., F.L., E.P., S.C., E.M.W.C., R.W.C., A.A.; DE-AC52-07NA27344 to J.A.K., P.D.]; National Cancer Institute [R01CA179243 to N.C., M.M.]; National Science Foundation [GEPR-1444202 to C.S.H., S.S., Q.Z.; MCB-1716285 to A.A.B., M.D.J.]; Horizon 2020 - Research and Innovation Framework Programme [686070 (DD-DeCaF) to M.E.B.]; Center for Individualized Medicine, Mayo Clinic [to M.M., N.C.]. Funding for open access charge: U.S. Department of Energy.
Publisher Copyright:
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
PY - 2021/1/8
Y1 - 2021/1/8
N2 - 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.
AB - 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.
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U2 - 10.1093/nar/gkaa746
DO - 10.1093/nar/gkaa746
M3 - Article
C2 - 32986834
AN - SCOPUS:85099399795
SN - 0305-1048
VL - 49
SP - D575-D588
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -