ArticleMetabolomics : Official journal of the Metabolomic Society2026
Metabolite names and identifiers: how far are we from interoperability?
Article in Metabolomics : Official journal of the Metabolomic Society, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
What it found
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The trial behind it
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Who cites it
2 citing papers in PubMed.
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
introductionToday, metabolomics literature suffers from ambiguity in metabolites’ nomenclature, making difficult intercomparison between publications and can lead to misinterpretations. Progress in the implementation of FAIR principles in metabolomics in various scientific communities is therefore imperative for successful comparisons across studies and for moving towards more large-scale metabolomics.
objectivesIn this context, the aim of the present work was to explore the potential ambiguities that may be introduced during metabolite contextualization and reporting, and finally provide operational guidelines for metabolite name and identifier conversion to increase interoperability in metabolomics.
methodsFrom a list of 100 frequently annotated metabolites in human plasma, but also relevant for plant sciences, several workflows based on different existing identifier conversion tools were set up and evaluated, using two alternative approaches, one from an experimenter and the other from a data scientist's perspective.
resultsFindings showed a high level of mismatches using metabolite names as input, whereas starting from identifiers showed heterogeneity in the conversion consistency, depending on the association between input identifiers, algorithm of the selected tool, their respective versions, as well as versions of databases used for mapping. Errors in cross-reference databases were also highlighted. Despite these facts, InChIKeys were found to provide the highest quality results using all identifier conversion tools.
conclusionFrom these results, operational guidelines were proposed using a curation process based on computational iterations, testing the stability and consistency of this conversion process, thus guaranteeing future metabolite contextualisation (e.g. links with pathways or phenotypes) and the interoperability of result reports.
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Registered trials
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