skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

Abstract 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 and KBase.

Authors:
ORCiD logo [1]; ORCiD logo [1];  [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [6]; ORCiD logo [7];  [7]; ORCiD logo [8]; ORCiD logo [9]; ORCiD logo [9]; ORCiD logo [9]; ORCiD logo [9]; ORCiD logo [10] more »; ORCiD logo [9]; ORCiD logo [1] « less
  1. Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
  2. Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
  3. Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
  4. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
  5. Department of Biology, Hope College, Holland, MI 49423, USA
  6. Department of Computer Science, Hope College, Holland, MI 49423, USA
  7. Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
  8. Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
  9. Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
  10. Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE; National Science Foundation (NSF); National Cancer Institute (NCI)
OSTI Identifier:
1668123
Alternate Identifier(s):
OSTI ID: 1669770
Grant/Contract Number:  
AC02–06CH11357; AC02–05CH11231; AC05–00OR22725; AC52–07NA27344; AC05-00OR22725; AC02-06CH11357; AC02-05CH11231; AC52-07NA27344; GEPR-1444202; MCB-1716285; R01CA17924
Resource Type:
Journal Article: Published Article
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Name: Nucleic Acids Research; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Seaver, Samuel M. D., Liu, Filipe, Zhang, Qizhi, Jeffryes, James, Faria, José P., Edirisinghe, Janaka N., Mundy, Michael, Chia, Nicholas, Noor, Elad, Beber, Moritz E., Best, Aaron A., DeJongh, Matthew, Kimbrel, Jeffrey A., D’haeseleer, Patrik, McCorkle, Sean R., Bolton, Jay R., Pearson, Erik, Canon, Shane, Wood-Charlson, Elisha M., Cottingham, Robert W., Arkin, Adam P., and Henry, Christopher S. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. United Kingdom: N. p., 2020. Web. doi:10.1093/nar/gkaa746.
Seaver, Samuel M. D., Liu, Filipe, Zhang, Qizhi, Jeffryes, James, Faria, José P., Edirisinghe, Janaka N., Mundy, Michael, Chia, Nicholas, Noor, Elad, Beber, Moritz E., Best, Aaron A., DeJongh, Matthew, Kimbrel, Jeffrey A., D’haeseleer, Patrik, McCorkle, Sean R., Bolton, Jay R., Pearson, Erik, Canon, Shane, Wood-Charlson, Elisha M., Cottingham, Robert W., Arkin, Adam P., & Henry, Christopher S. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. United Kingdom. doi:10.1093/nar/gkaa746.
Seaver, Samuel M. D., Liu, Filipe, Zhang, Qizhi, Jeffryes, James, Faria, José P., Edirisinghe, Janaka N., Mundy, Michael, Chia, Nicholas, Noor, Elad, Beber, Moritz E., Best, Aaron A., DeJongh, Matthew, Kimbrel, Jeffrey A., D’haeseleer, Patrik, McCorkle, Sean R., Bolton, Jay R., Pearson, Erik, Canon, Shane, Wood-Charlson, Elisha M., Cottingham, Robert W., Arkin, Adam P., and Henry, Christopher S. Mon . "The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes". United Kingdom. doi:10.1093/nar/gkaa746.
@article{osti_1668123,
title = {The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes},
author = {Seaver, Samuel M. D. and Liu, Filipe and Zhang, Qizhi and Jeffryes, James and Faria, José P. and Edirisinghe, Janaka N. and Mundy, Michael and Chia, Nicholas and Noor, Elad and Beber, Moritz E. and Best, Aaron A. and DeJongh, Matthew and Kimbrel, Jeffrey A. and D’haeseleer, Patrik and McCorkle, Sean R. and Bolton, Jay R. and Pearson, Erik and Canon, Shane and Wood-Charlson, Elisha M. and Cottingham, Robert W. and Arkin, Adam P. and Henry, Christopher S.},
abstractNote = {Abstract 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 and KBase.},
doi = {10.1093/nar/gkaa746},
journal = {Nucleic Acids Research},
issn = {0305-1048},
number = ,
volume = ,
place = {United Kingdom},
year = {2020},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1093/nar/gkaa746

Save / Share:

Works referenced in this record:

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks
journal, November 2013


Metabolic Reconstruction and Modeling Microbial Electrosynthesis
journal, August 2017


Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen
journal, January 2016

  • Marcellin, Esteban; Behrendorff, James B.; Nagaraju, Shilpa
  • Green Chemistry, Vol. 18, Issue 10
  • DOI: 10.1039/C5GC02708J

Metabolic engineering of Escherichia coli for the de novo stereospecific biosynthesis of 1,2-propanediol through lactic acid
journal, June 2019


BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
journal, October 2015

  • King, Zachary A.; Lu, Justin; Dräger, Andreas
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1049

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics
journal, August 2015

  • Jeffryes, James G.; Colastani, Ricardo L.; Elbadawi-Sidhu, Mona
  • Journal of Cheminformatics, Vol. 7, Issue 1
  • DOI: 10.1186/s13321-015-0087-1

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks
journal, August 2008

  • Jankowski, Matthew D.; Henry, Christopher S.; Broadbelt, Linda J.
  • Biophysical Journal, Vol. 95, Issue 3
  • DOI: 10.1529/biophysj.107.124784

High-throughput generation, optimization and analysis of genome-scale metabolic models
journal, August 2010

  • Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A.
  • Nature Biotechnology, Vol. 28, Issue 9
  • DOI: 10.1038/nbt.1672

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
journal, May 2012


In silico metabolic engineering of Clostridium ljungdahlii for synthesis gas fermentation
journal, November 2016


A systematic assessment of current genome-scale metabolic reconstruction tools
journal, August 2019


Computational analysis of the productivity potential of CAM
journal, February 2018


Data, information, knowledge and principle: back to metabolism in KEGG
journal, November 2013

  • Kanehisa, Minoru; Goto, Susumu; Sato, Yoko
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1076

Towards a genome-scale kinetic model of cellular metabolism
journal, January 2010

  • Smallbone, Kieran; Simeonidis, Evangelos; Swainston, Neil
  • BMC Systems Biology, Vol. 4, Issue 1
  • DOI: 10.1186/1752-0509-4-6

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
journal, November 2015

  • Caspi, Ron; Billington, Richard; Ferrer, Luciana
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1164

A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase
journal, December 2018

  • Lieven, Christian; Petersen, Leander A. H.; Jørgensen, Sten Bay
  • Frontiers in Microbiology, Vol. 9
  • DOI: 10.3389/fmicb.2018.02947

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains
journal, December 2016

  • Khodayari, Ali; Maranas, Costas D.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms13806

ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling
journal, September 2018


Global phenotypic characterization of bacteria
journal, January 2009


Optimization based automated curation of metabolic reconstructions
journal, January 2007

  • Satish Kumar, Vinay; Dasika, Madhukar S.; Maranas, Costas D.
  • BMC Bioinformatics, Vol. 8, Issue 1
  • DOI: 10.1186/1471-2105-8-212

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
journal, June 2014

  • Seaver, Samuel M. D.; Gerdes, Svetlana; Frelin, Océane
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 26
  • DOI: 10.1073/pnas.1401329111

Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets
journal, August 2016


MEMOTE for standardized genome-scale metabolic model testing
journal, March 2020

  • Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.
  • Nature Biotechnology, Vol. 38, Issue 3
  • DOI: 10.1038/s41587-020-0446-y

Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

Modeling central metabolism and energy biosynthesis across microbial life
journal, August 2016


The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
journal, October 2003


A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C 3 and Crassulacean Acid Metabolism Leaves
journal, March 2014

  • Cheung, C. Y. Maurice; Poolman, Mark G.; Fell, David. A.
  • Plant Physiology, Vol. 165, Issue 2
  • DOI: 10.1104/pp.113.234468

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
journal, November 2014


ExplorEnz: the primary source of the IUBMB enzyme list
journal, January 2009

  • McDonald, A. G.; Boyce, S.; Tipton, K. F.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn582

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations
journal, January 2009

  • Henry, Christopher S.; Zinner, Jenifer F.; Cohoon, Matthew P.
  • Genome Biology, Vol. 10, Issue 6
  • DOI: 10.1186/gb-2009-10-6-r69

PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency
journal, August 2018

  • Seaver, Samuel M. D.; Lerma‐Ortiz, Claudia; Conrad, Neal
  • The Plant Journal, Vol. 95, Issue 6
  • DOI: 10.1111/tpj.14003

Experimental testing of a spatiotemporal metabolic model for carbon monoxide fermentation with Clostridium autoethanogenum
journal, January 2018


KEGG as a reference resource for gene and protein annotation
journal, October 2015

  • Kanehisa, Minoru; Sato, Yoko; Kawashima, Masayuki
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1070

Improving prediction fidelity of cellular metabolism with kinetic descriptions
journal, December 2015


Metagenome level metabolic network reconstruction analysis reveals the microbiome in the Bogotá River is functionally close to the microbiome in produced water
journal, May 2019


Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes
journal, November 2018


Network-based metabolic analysis and microbial community modeling
journal, June 2016


In silico aided metabolic engineering of Klebsiella oxytoca and fermentation optimization for enhanced 2,3-butanediol production
journal, June 2013

  • Park, Jong Myoung; Song, Hyohak; Lee, Hee Jong
  • Journal of Industrial Microbiology & Biotechnology, Vol. 40, Issue 9
  • DOI: 10.1007/s10295-013-1298-y

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
journal, January 2011

  • Bordbar, Aarash; Feist, Adam M.; Usaite-Black, Renata
  • BMC Systems Biology, Vol. 5, Issue 1
  • DOI: 10.1186/1752-0509-5-180

Long-term phenotypic evolution of bacteria
journal, October 2014

  • Plata, Germán; Henry, Christopher S.; Vitkup, Dennis
  • Nature, Vol. 517, Issue 7534
  • DOI: 10.1038/nature13827

KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018

  • Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S.
  • Nature Biotechnology, Vol. 36, Issue 7
  • DOI: 10.1038/nbt.4163

Reframing gene essentiality in terms of adaptive flexibility
journal, December 2018


The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
journal, September 2005


Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation
journal, March 2017

  • Mendoza, Sebastián N.; Cañón, Pablo M.; Contreras, Ángela
  • Frontiers in Microbiology, Vol. 8
  • DOI: 10.3389/fmicb.2017.00534

Open Babel: An open chemical toolbox
journal, October 2011

  • O'Boyle, Noel M.; Banck, Michael; James, Craig A.
  • Journal of Cheminformatics, Vol. 3, Issue 1
  • DOI: 10.1186/1758-2946-3-33

Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction: COMMUNITY DATA-DRIVEN METABOLIC NETWORK MODELING
journal, June 2016

  • Henry, Christopher S.; Bernstein, Hans C.; Weisenhorn, Pamela
  • Journal of Cellular Physiology, Vol. 231, Issue 11
  • DOI: 10.1002/jcp.25428

Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti
journal, July 2016

  • diCenzo, George C.; Checcucci, Alice; Bazzicalupo, Marco
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12219

Rewriting yeast central carbon metabolism for industrial isoprenoid production
journal, September 2016

  • Meadows, Adam L.; Hawkins, Kristy M.; Tsegaye, Yoseph
  • Nature, Vol. 537, Issue 7622
  • DOI: 10.1038/nature19769

Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolism
journal, January 2010

  • Jerby, Livnat; Shlomi, Tomer; Ruppin, Eytan
  • Molecular Systems Biology, Vol. 6, Issue 1
  • DOI: 10.1038/msb.2010.56

Model-based metabolic engineering enables high yield itaconic acid production by Escherichia coli
journal, November 2016


Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm
journal, March 2015

  • Seaver, Samuel M. D.; Bradbury, Louis M. T.; Frelin, Océane
  • Frontiers in Plant Science, Vol. 6
  • DOI: 10.3389/fpls.2015.00142

Towards automatic classification within the ChEBI ontology
journal, July 2009


Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
journal, May 2005


Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity
journal, June 2016

  • Bosi, Emanuele; Monk, Jonathan M.; Aziz, Ramy K.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 26
  • DOI: 10.1073/pnas.1523199113

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics
journal, April 2017

  • Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe
  • Scientific Reports, Vol. 7, Issue 1
  • DOI: 10.1038/srep46249

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks
journal, January 2013


Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1)
journal, November 2015

  • de la Torre, Andrea; Metivier, Aisha; Chu, Frances
  • Microbial Cell Factories, Vol. 14, Issue 1
  • DOI: 10.1186/s12934-015-0377-3

Combining multiple functional annotation tools increases coverage of metabolic annotation
journal, December 2018


Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints
journal, August 2013

  • Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher
  • Biotechnology Journal, Vol. 8, Issue 9
  • DOI: 10.1002/biot.201300091

Using systems biology approaches to elucidate cause and effect in host–microbiome interactions
journal, June 2017

  • Witherden, Elizabeth A.; Moyes, David L.; Bruce, Kenneth D.
  • Current Opinion in Systems Biology, Vol. 3
  • DOI: 10.1016/j.coisb.2017.05.003

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052
journal, January 2011

  • Milne, Caroline B.; Eddy, James A.; Raju, Ravali
  • BMC Systems Biology, Vol. 5, Issue 1
  • DOI: 10.1186/1752-0509-5-130

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
journal, January 2012

  • Kumar, Akhil; Suthers, Patrick F.; Maranas, Costas D.
  • BMC Bioinformatics, Vol. 13, Issue 1
  • DOI: 10.1186/1471-2105-13-6