ChEBI, a comprehensive database and ontology of chemical entities of biological interest, has seen significant improvements and additions in 2016. The database now includes over 46,000 entries, with a substantial increase in the number of fully curated entries, particularly in the area of endogenous metabolites for various organisms such as human, mouse, Escherichia coli, and yeast. The ontology classification of metabolites has been extended and revised to better represent these compounds, including updates to nomenclature recommendations. The user interface has been reworked to improve the user experience, removing the dependency on Java applets and adopting embedded JavaScript components. The website has transitioned from a monthly release cycle to a 'live' content stream, ensuring that new content is immediately visible and accessible. Programmatic access has been enhanced with the introduction of libChEBI, a library available in Java, Python, and Matlab. Two new tools have been added: BiNChE, a web-based enrichment analysis tool for the ChEBI ontology, and OntoQuery, a web-based tool for executing complex logical queries against the ChEBI ontology. These tools support statistical analysis and query formulation, respectively, making ChEBI more versatile for various scientific applications. Overall, these updates and additions have further solidified ChEBI's position as an essential resource in bioinformatics and chemistry.ChEBI, a comprehensive database and ontology of chemical entities of biological interest, has seen significant improvements and additions in 2016. The database now includes over 46,000 entries, with a substantial increase in the number of fully curated entries, particularly in the area of endogenous metabolites for various organisms such as human, mouse, Escherichia coli, and yeast. The ontology classification of metabolites has been extended and revised to better represent these compounds, including updates to nomenclature recommendations. The user interface has been reworked to improve the user experience, removing the dependency on Java applets and adopting embedded JavaScript components. The website has transitioned from a monthly release cycle to a 'live' content stream, ensuring that new content is immediately visible and accessible. Programmatic access has been enhanced with the introduction of libChEBI, a library available in Java, Python, and Matlab. Two new tools have been added: BiNChE, a web-based enrichment analysis tool for the ChEBI ontology, and OntoQuery, a web-based tool for executing complex logical queries against the ChEBI ontology. These tools support statistical analysis and query formulation, respectively, making ChEBI more versatile for various scientific applications. Overall, these updates and additions have further solidified ChEBI's position as an essential resource in bioinformatics and chemistry.