ChEBI

ChEBI, short for Chemical Entities of Biological Interest, is a freely accessible database and ontology of small molecular entities used in biological contexts. It is curated and maintained by the European Bioinformatics Institute (EMBL-EBI). The resource provides a stable, machine-readable vocabulary for chemical substances that participate in biological processes, metabolism, or signaling, along with detailed data about each entity.

Entries in ChEBI include metabolites, cofactors, ions, natural products, and synthetic compounds. Each entry has a unique CHEBI identifier, a preferred name, and a set of synonyms, as well as chemical information such as molecular formula, exact mass, charge, and structural representations (SMILES, InChI, InChIKey). Entries are linked through an ontology with relationships such as is_a, part_of, or has_role, enabling hierarchical queries and semantic reasoning.

ChEBI provides access via a web interface and programmatic REST API. Data can be searched by name, synonym, or CHEBI ID, and downloadable data are available in formats suitable for integration with other bioinformatics resources (ontology formats like OBO/OWL and data dumps). It is widely used to annotate biological databases, curate pathway and metabolite annotations, and support workflows that require consistent chemical identifiers across studies.

ChEBI is part of the ecosystem of biological ontologies and is cross-referenced with other chemical databases and resources. Its standardized vocabulary helps harmonize chemical nomenclature in genomics, proteomics, metabolomics, and systems biology, and it continues to expand through manual curation and community input.