ChEBI is a database and ontology containing information about chemical entities of biological interest. It includes over 46,000 entries, each classified within the ontology and annotated with chemical structures, cross-references, synonyms, and literature citations. The database is freely available online at http://www.ebi.ac.uk/chebi. In 2016, ChEBI underwent significant improvements, including an expanded collection of endogenous metabolites for several organisms, such as human, mouse, Escherichia coli, and yeast. The user interface was reworked to improve the user experience, replacing Java applets with JavaScript components and moving from monthly updates to a 'live' website. A new library, libChEBI, was introduced for programmatic access in Java, Python, and Matlab. Two new tools, BiNChE and OntoQuery, were added. BiNChE is an analysis tool for metabolomics data, while OntoQuery is a query tool for the ontology. ChEBI is widely used in bioinformatics, systems biology, and text mining, and is integrated with other ontologies such as the Gene Ontology. The database also includes cross-references to other metabolome databases and has been updated to reflect current nomenclature recommendations. The ChEBI public web application has been reworked to improve the user experience, with a focus on page layout, responsiveness, and interactive features. The database now contains 14,489 metabolites across 2114 distinct species. ChEBI is funded by the BBSRC and is available for free use.ChEBI is a database and ontology containing information about chemical entities of biological interest. It includes over 46,000 entries, each classified within the ontology and annotated with chemical structures, cross-references, synonyms, and literature citations. The database is freely available online at http://www.ebi.ac.uk/chebi. In 2016, ChEBI underwent significant improvements, including an expanded collection of endogenous metabolites for several organisms, such as human, mouse, Escherichia coli, and yeast. The user interface was reworked to improve the user experience, replacing Java applets with JavaScript components and moving from monthly updates to a 'live' website. A new library, libChEBI, was introduced for programmatic access in Java, Python, and Matlab. Two new tools, BiNChE and OntoQuery, were added. BiNChE is an analysis tool for metabolomics data, while OntoQuery is a query tool for the ontology. ChEBI is widely used in bioinformatics, systems biology, and text mining, and is integrated with other ontologies such as the Gene Ontology. The database also includes cross-references to other metabolome databases and has been updated to reflect current nomenclature recommendations. The ChEBI public web application has been reworked to improve the user experience, with a focus on page layout, responsiveness, and interactive features. The database now contains 14,489 metabolites across 2114 distinct species. ChEBI is funded by the BBSRC and is available for free use.