Evidence map›Paper›PMID 42556124›Full record

ReviewCurrent opinion in biotechnology2026

Computational metabolomics at scale: from open data to insight.

Ewy A Mathé, Justin Jj van der Hooft, Haley Chatelaine, Louis-Félix Nothias, Stacey N Reinke, Juan Antonio Vizcaíno, Egon L Willighagen, Timothy Md Ebbels, Soha Hassoun

Abstract readReview
In one paragraph

Review in Current opinion in biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Ewy A MathéDivision of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA. Electronic address: ewy.mathe@nih.gov.
Justin Jj van der HooftBioinformatics Group, Wageningen University & Research, Wageningen 6708PB, the Netherlands; Department of Biochemistry, University of Johannesburg, Johannesburg 2006, South Africa.
Haley ChatelaineDivision of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
Louis-Félix NothiasUniversité Côte d'Azur, CNRS, ICN, Nice, France; Interdisciplinary Institute for Artificial Intelligence (3iA) Côte d'Azur, Sophia-Antipolis, France.
Stacey N ReinkeSchool of Science, Edith Cowan University, Joondalup 6027, Australia.
Juan Antonio VizcaínoEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Egon L WillighagenDepartment of Translational Genomics, NUTRIM, Maastricht University, Maastricht, the Netherlands.
Timothy Md EbbelsSection of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK.
Soha HassounDepartment of Computer Science, Tufts University, Medford, MA 02155, United States; Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, United States.

Funding

Deep Learning Models for Metabolomics AnalysisR35GM148219 · NIGMS · TUFTS UNIVERSITY MEDFORD · PI Soha Hassoun · 2023 to 2026
$1.4M
Metabolomics and multi-omicsZICTR000547 · NCATS · NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES · PI MATHÉ, EWY · 2025 to 2025
$978k
Intramural NIH HHS ZIA TR000547Intramural NIH HHS ZIC TR000547NIGMS NIH HHS R35 GM148219
6 · The paper itself

Abstract

Metabolomics data are currently generated at scale thanks to the evolution of technologies that have led to marked improvements in the number of metabolites detected, spanning all chemical classes. These data are increasingly submitted to public repositories for data reuse, integration, and interpretation. Despite the availability of public resources and associated computational tools, the field still lacks a widely adopted, consistent data and analytics infrastructure capable of transforming this wealth of information into scientific insight. Indeed, the metabolomics field is just now scratching the surface of being able to harness the power of new computational technologies. In this review, we summarize discussions from the "Dagstuhl-Seminar 24181 Computational Metabolomics: Towards Molecules, Models, and their Meaning" with a focus on public data availability, open data standards, data and knowledge integration, and education. Our goal is to raise awareness and adoption of the latest open science resources while highlighting key areas needing further development.

Indexed as

Computational BiologyMetabolomicsHumans

Identifiers

PMID42556124
PMCPMC13592028

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.