ModelSEED Biochemistry Database
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.
Description
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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.
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Webpage:
https://modelseed.org/biochemWebpage
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https://modelseed.org/biochem
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence:
Name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)Licence name
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Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
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https://creativecommons.org/licenses/by-nc/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
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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
PMID: 32986834
metasource: Fairsharing.org
version: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications
More detailed information about this field from each metasource.
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
PMID: 32986834
metasource: Fairsharing.org
version: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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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
PubMed citations: 29.
29 articles citing: The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models. PMID:35694833
Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges. PMID:35625648
Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes. PMID:35547116
KEMET - A python tool for KEGG Module evaluation and microbial genome annotation expansion. PMID:35422973
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. PMID:35322036
Systems Biology of Gut Microbiota-Human Receptor Interactions: Toward Anti-inflammatory Probiotics. PMID:35308387
Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation. PMID:35207655
CobraMod: A pathway-centric curation tool for constraint-based metabolic models. PMID:35201291
Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models. PMID:35196325
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. PMID:35130271
TrpNet: Understanding Tryptophan Metabolism across Gut Microbiome. PMID:35050132
eQuilibrator 3.0: a database solution for thermodynamic constant estimation. PMID:34850162
Artificial Intelligence for Autonomous Molecular Design: A Perspective. PMID:34833853
A gap-filling algorithm for prediction of metabolic interactions in microbial communities. PMID:34723959
Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern. PMID:34681003
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. PMID:34625561
Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis. PMID:34609164
Modelling microbial communities: Harnessing consortia for biotechnological applications. PMID:34584635
Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19. PMID:34353886
Functional prediction of environmental variables using metabolic networks. PMID:34108539
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. PMID:33918864
Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis. PMID:33879809
Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions. PMID:33869975
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. PMID:33691770
Metabolic Modeling to Interrogate Microbial Disease: A Tale for Experimentalists. PMID:33681294
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis. PMID:33602294
Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations. PMID:33467644
The 2021 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:33396976
Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. PMID:33372654
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computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
data retrieval
metasource: Fairsharing.org
version: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
mathematical model
metasource: Fairsharing.org
version: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
modeling and simulation
metasource: Fairsharing.org
version: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
network model
metasource: Fairsharing.org
version: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
reaction data
metasource: Fairsharing.org
version: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Tags
More detailed information about this field from each metasource.
computational predictions
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
data retrieval
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
mathematical model
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
modeling and simulation
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
network model
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
reaction data
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
computational predictions data retrieval genome mathematical model modeling and simulation network model reaction data
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