Sébastien Moretti, Anne Niknejad, Marco Pagni, Florence Mehl
MetaNetX (https://www.metanetx.org/) is a comprehensive resource for the reconciliation and integration of metabolic information across diverse biochemical databases. The 2025 update significantly enhances chemical and reaction coverage, incorporating new data and refining chemical structure computation and normalization. These improvements support more accurate reconciliation across sources and enable robust multi-omics integration through standardized identifiers (InChI, SMILES) and curated R-group definitions. The Resource Description Format (RDF) graph has been expanded to capture reconciliation history, and the SPARQL endpoint now includes enriched documentation and example queries, facilitating programmatic access and integration with AI tools. Together, these developments reinforce MetaNetX as a high-quality, open-access platform for systems biology, metabolic modeling, and multi-omics data analysis.