MetExplore 3: a web solution for network-based interpretation of metabolomics data
Year: 2026
Type: conference-paper
Abstract: Introduction: Metabolomics experiments routinely generate lists of metabolites (metabolic profiles), but transforming these results into biologically interpretable metabolic mechanisms remains challenging. Existing workflows or web solutions often rely on disconnected tools for identifier search, pathway enrichment, network extraction, visualization, and dissemination of results.Aim: We developed MetExplore 3 to provide an integrated web platform for the exploration, contextualization, visualization, and sharing of graphical representation of metabolomics data mapping within genome-scale metabolic networks.Methods: MetExplore 3 is an open access web server based on modern web components that provides interactive tools for metabolic network analysis and visualization. The platform includes published curated genome-scale metabolic networks for several organisms and also allows users to import their own metabolic networks from SBML files. A dedicated metabolite identification module maps experimental metabolites onto metabolic networks using ChEBI identifiers. Once mapped, metabolites can be analyzed through pathway overrepresentation approaches and used to extract biologically contextualized subnetworks. These subnetworks can then be interactively visualized, edited, and shared through reproducible graphical representations. In addition to the graphical interface, MetExplore 3 provides an API enabling access to data structures and analytical methods from external environments and programming languages, facilitating integration into custom bioinformatics workflows.Results: MetExplore 3 enables users to move from metabolite identification to interpretable and shareable metabolic network representations within a unified environment, providing an alternative to widely used pathway enrichment interpretations. The platform integrates metabolite mapping, pathway overrepresentation, subnetwork extraction, and interactive visualization into a unique web solution. The ability to save and share curated network layouts facilitates collaborative interpretation of metabolomics data.Conclusion: By integrating analytical, visualization, and sharing functionalities within the same web solution, MetExplore 3 helps bridge the gap between metabolite lists and biologically meaningful network interpretations. The platform provides the metabolomics community with an accessible and extensible environment for network-based analysis of metabolomics data.
Source: HAL
Institutions: Toxicologie Alimentaire, MetaboHUB
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7205394822