ArticleNucleic acids research2021
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 137 papers.
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Who cites it
137 citing papers in PubMed.
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- Metabolic Modelling Facilitates the Design of Synthetic Communities by Simplifying Natural Microbial Communities.Environmental microbiology · 2026Article
- Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition.Nature communications · 2026Article
- Integrated multi-dimensional modeling of non-model bacteria identifies engineering targets for acarbose biosynthesis optimization.Cell reports methods · 2026Article
- Nutrient control enables metabolic reconstruction ofbioRxiv : the preprint server for biology · 2026Article
- Genome-scale metabolic model guided metabolic flux analysis in the endophyte Alternaria burnsii NCIM1409.Bioprocess and biosystems engineering · 2026Article
- Predictive Algal Systems Biology: Integrating Omics, Genome-Scale Metabolic Models, and Machine Learning.Bioengineering (Basel, Switzerland) · 2026Review
- Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis.BMC bioinformatics · 2026Article
- Hypergraph learning with multi-dimensional metabolite feature extractions and static-dynamic attention mechanisms to fill missing reactions in metabolic networks.Briefings in bioinformatics · 2026Article
- High-throughput generation and comparison of genome-scale metabolic models reveal strain-specific metabolic diversity in 439mSystems · 2026Article
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Reconstruction of human metabolic models with large language models.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A Novel Topology-Based Candidate Reaction Prediction Approach for Gap-Fillings of Genome-Scale Metabolic Models.Metabolites · 2026Article
- Effects of the Synbiotic Formulation EDC-HHA01 on Glucose Regulation in Adults with Type 2 Diabetes and Prediabetes: A Randomized, Placebo-Controlled Study.Microorganisms · 2026Article
- Modeling neutrophilic iron-oxidizing bacteria: a KBase narrative resource describing newly integrated metabolic reactions.Microbiology resource announcements · 2026Article
- LumbriCyc: towards metabolic modelling of earthworms.NPJ systems biology and applications · 2026Article
- Revealing interactions between microbes, metabolites, and dietary compounds using genome-scale analysis.Microbiome · 2026Article
77 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
22 authors.
Funding
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/biochem and KBase.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.