ReviewArchives of toxicology2011
A survey of metabolic databases emphasizing the MetaCyc family.
Review in Archives of toxicology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
32 citing papers in PubMed.
- Dynamic changes of volatile substances and their driving factors during curing and fermentation of Hainan cigar.Bioresources and bioprocessing · 2026Article
- Phosphate deprivation restricts bacterial degradation of the marine polysaccharide fucoidan.Nature microbiology · 2026Article
- Identifying dormancy-associated enzymes in Mycobacterium tuberculosis through a computational pipeline integrating flux balance analysis and metabolic modeling.Molecular diversity · 2026Article
- Microbiome Single Cell Atlases Generated with a Commercial Instrument.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Elucidation of bacterial trehalose-degrading trehalase and trehalose phosphorylase: physiological significance and its potential applications.Glycobiology · 2024Review
- Colonic in vitro fermentation of mycoprotein promotes shifts in gut microbiota, with enrichment of Bacteroides species.Communications biology · 2024Article
- Microbiome single cell atlases generated with a commercial instrument.Research square · 2023Article
- Genomic insights into the c-di-GMP signaling and biofilm development in the saprophytic spirochete Leptospira biflexa.Archives of microbiology · 2023Article
- Urine and FecalMetabolites · 2022Article
- Prediction of trehalose-metabolic pathway and comparative analysis of KEGG, MetaCyc, and RAST databases based on complete genome of Variovorax sp. PAMC28711.BMC genomic data · 2022Article
- Pathway information extracted from 25 years of pathway figures.Genome biology · 2020Article
- SAMMI: a semi-automated tool for the visualization of metabolic networks.Bioinformatics (Oxford, England) · 2020Article
- NMR and MS-based Stable Isotope-Resolved Metabolomics and Applications in Cancer Metabolism.Trends in analytical chemistry : TRAC · 2019Article
- Use of Metabolomics in Improving Assessment of Dietary Intake.Clinical chemistry · 2018Review
- SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases.Database : the journal of biological databases and curation · 2018Article
- Article
- ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods.Database : the journal of biological databases and curation · 2016Article
- Computational Metabolomics Operations at BioCyc.org.Metabolites · 2015Article
- Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam.BMC evolutionary biology · 2014Article
- VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera).Frontiers in plant science · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Thanks to the confluence of genome sequencing and bioinformatics, the number of metabolic databases has expanded from a handful in the mid-1990s to several thousand today. These databases lie within distinct families that have common ancestry and common attributes. The main families are the MetaCyc, KEGG, Reactome, Model SEED, and BiGG families. We survey these database families, as well as important individual metabolic databases, including multiple human metabolic databases. The MetaCyc family is described in particular detail. It contains well over 1,000 databases, including highly curated databases for Escherichia coli, Saccharomyces cerevisiae, Mus musculus, and Arabidopsis thaliana. These databases are available through a number of web sites that offer a range of software tools for querying and visualizing metabolic networks. These web sites also provide multiple tools for analysis of gene expression and metabolomics data, including visualization of those datasets on metabolic network diagrams and over-representation analysis of gene sets and metabolite sets.
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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.