ArticleMetabolites2019
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling.
Article in Metabolites, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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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
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- BioprospectingFrontiers in fungal biology · 2021Pooled it
- Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz.Molecular systems biology · 2026Article
- Metabolite names and identifiers: how far are we from interoperability?Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Securing the Future of NMR Metabolomics Reproducibility: A Call for Standardized Reporting.Analytical chemistry · 2025Review
- How to crack a SMILES: automatic crosschecked chemical structure resolution across multiple services using MoleculeResolver.Journal of cheminformatics · 2025Article
- CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters.Nature communications · 2025Article
- Physiology-informed use of Cupriavidus necator in biomanufacturing: a review of advances and challenges.Microbial cell factories · 2025Review
- Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches.NPJ systems biology and applications · 2024Article
- Article
- Microbiome modeling: a beginner's guide.Frontiers in microbiology · 2024Review
- Standards, dissemination, and best practices in systems biology.Current opinion in biotechnology · 2023Review
- Reconciliation and evolution of Penicillium rubens genome-scale metabolic networks-What about specialised metabolism?PloS one · 2023Article
- Review of Current Human Genome-Scale Metabolic Models for Brain Cancer and Neurodegenerative Diseases.Cells · 2022Review
- A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications.PLoS computational biology · 2022Article
- Dissecting carbon metabolism ofComputational and structural biotechnology journal · 2022Article
- Article
- Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis.PLoS computational biology · 2021Article
- Hierarchical Harmonization of Atom-Resolved Metabolic Reactions across Metabolic Databases.Metabolites · 2021Article
- Multi-omics integration in biomedical research - A metabolomics-centric review.Analytica chimica acta · 2021Review
- Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks.Nucleic acids research · 2020Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Genome-scale metabolic models (GEMs) are manually curated repositories describing the metabolic capabilities of an organism. GEMs have been successfully used in different research areas, ranging from systems medicine to biotechnology. However, the different naming conventions (namespaces) of databases used to build GEMs limit model reusability and prevent the integration of existing models. This problem is known in the GEM community, but its extent has not been analyzed in depth. In this study, we investigate the name ambiguity and the multiplicity of non-systematic identifiers and we highlight the (in)consistency in their use in 11 biochemical databases of biochemical reactions and the problems that arise when mapping between different namespaces and databases. We found that such inconsistencies can be as high as 83.1%, thus emphasizing the need for strategies to deal with these issues. Currently, manual verification of the mappings appears to be the only solution to remove inconsistencies when combining models. Finally, we discuss several possible approaches to facilitate (future) unambiguous mapping.
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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.