ReviewFEMS microbiology letters2013
The challenge of constructing, classifying, and representing metabolic pathways.
Review in FEMS microbiology letters, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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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
49 citing papers in PubMed.
- Trial
- Phosphate deprivation restricts bacterial degradation of the marine polysaccharide fucoidan.Nature microbiology · 2026Article
- The genome-scale sugar metabolic model fromCurrent research in microbial sciences · 2026Article
- Proteomic profiling of zinc homeostasis mechanisms in Pseudomonas aeruginosa through data-dependent and data-independent acquisition mass spectrometry.Metallomics : integrated biometal science · 2025Article
- Microbiome Single Cell Atlases Generated with a Commercial Instrument.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Proteomic profiling of zinc homeostasis mechanisms inbioRxiv : the preprint server for biology · 2025Article
- Integrative physiological, biochemical, and metabolomic analyses reveal complex drought and zinc stress tolerance in a novelFrontiers in plant science · 2025Article
- Integrated multi-omic approach reveals the effect of a Graminaceae-derived biostimulant and its lighter fraction on salt-stressed lettuce plants.Scientific reports · 2024Article
- Colonic in vitro fermentation of mycoprotein promotes shifts in gut microbiota, with enrichment of Bacteroides species.Communications biology · 2024Article
- Veterinary systems biology for bridging the phenotype-genotype gap via computational modeling for disease epidemiology and animal welfare.Briefings in bioinformatics · 2024Review
- A multi-omics approach to unravel the interaction between heat and drought stress in theFrontiers in plant science · 2024Article
- md_harmonize: A Python Package for Atom-Level Harmonization of Public Metabolic Databases.Metabolites · 2023Article
- Microbiome single cell atlases generated with a commercial instrument.Research square · 2023Article
- Metabolomics Insight into the Variety-Mediated Responses toACS omega · 2023Article
- Exploring the Interplay between Metabolic Pathways and Taxane Production in ElicitedPlants (Basel, Switzerland) · 2023Article
- Plasmon-activated water as a therapeutic strategy in Alzheimer's disease by altering gut microbiota.Aging · 2023Article
- Sparse tree-based clustering of microbiome data to characterize microbiome heterogeneity in pancreatic cancer.Journal of the Royal Statistical Society. Series C, Applied statistics · 2023Article
- Article
- Integrated Metabolomics and Morpho-Biochemical Analyses Reveal a Better Performance ofInternational journal of molecular sciences · 2022Article
- Biochemical Insights into the Ability ofPlants (Basel, Switzerland) · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Scientists, educators, and students benefit from having free and centralized access to the wealth of metabolic information that has been gathered over the decades. Curators of the MetaCyc database work to present this information in an easily understandable pathway-based framework. MetaCyc is used not only as an encyclopedic resource for metabolic information but also as a template for the pathway prediction software that generates pathway/genome databases for thousands of organisms with sequenced genomes (available at www.biocyc.org). Curators need to define pathway boundaries and classify pathways within a broader pathway ontology to maximize the utility of the pathways to both users and the pathway prediction software. These seemingly simple tasks pose several challenges. This review describes these challenges as well as the criteria that need to be considered, and the rules that have been developed by MetaCyc curators as they make decisions regarding the representation and classification of metabolic pathway information in MetaCyc. The functional consequences of these decisions in regard to pathway prediction in new species are also discussed.
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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.