EMBL-EBIChemical Entities of Biological Interest (ChEBI) is a freely available database and ontology of molecular entities maintained by the European Bioinformatics Institute (EMBL-EBI). Covering over 195,000 chemical entities, ChEBI provides a structured classification of small molecules relevant to biology, from metabolites and drugs to environmental chemicals, using internationally standardized nomenclature.
Background
ChEBI was developed at the European Bioinformatics Institute as part of the Open Biomedical Ontologies (OBO) effort, with the first formal description published in 2008. The project was motivated by the need for a freely available, expertly curated chemical ontology that could serve as a reference vocabulary for chemical entities encountered in biological research. Prior to ChEBI, chemical databases were typically either proprietary or lacked the ontological structure needed for computational reasoning about chemical relationships.
ChEBI distinguishes itself from other chemical databases by its focus on biological relevance and its incorporation of an ontological classification. Macromolecules directly encoded by the genome, such as nucleic acids and proteins, are excluded; ChEBI focuses on small chemical compounds and related entities.
Purpose & Scope
ChEBI serves as both a database and an ontology. As a database, it provides detailed information about individual chemical entities including:
- Systematic and common names following IUPAC and NC-IUBMB nomenclature
- Molecular formulae, InChI strings, and SMILES representations
- Cross-references to other databases (PubChem, ChEMBL, DrugBank, KEGG, etc.)
- Literature citations and species data
As an ontology, ChEBI organizes entities into a classification hierarchy that enables queries based on chemical class (e.g., "amino acid," "carbohydrate") and biological role (e.g., "enzyme inhibitor," "neurotransmitter"). This dual nature makes ChEBI valuable both for record-level chemical identification and for higher-level reasoning about chemical categories.
Key Statistics
| Metric | Value |
|---|---|
| Total entries | 195,000+ |
| Manually curated | Three-star entries (fully curated) |
| Nomenclature standard | IUPAC / NC-IUBMB |
| Part of | OBO Foundry |
Serializations & Technical Formats
ChEBI is available in multiple formats: OBO format and OWL for the ontological classification, SDF for chemical structure data, and flat file and SQL dump formats for the full database. Data can also be accessed through web services and a SPARQL endpoint. All downloads are available from the ChEBI website.
Governance & Maintenance
ChEBI is maintained by the ChEBI team at the European Bioinformatics Institute (EMBL-EBI), part of the European Molecular Biology Laboratory. Curation follows a three-tier quality system: one-star entries are automatically generated, two-star entries have been checked by a curator, and three-star entries have been fully manually curated with verified chemical structures and complete annotation. Community submissions are accepted through the ChEBI Submission Portal.
ChEBI is a member of the OBO Foundry, following its principles for open, interoperable ontology development.
Notable Implementations
ChEBI identifiers are widely used across biological databases as the standard reference for small molecule identification. They appear in UniProt, Reactome, MetaboLights, IntEnz, and many pathway and metabolomics databases. ChEBI terms are used in GO annotations to specify chemical participants in molecular functions and biological processes. The ontology is also integrated into the EMBL-EBI Ontology Lookup Service (OLS).
Related Standards
- Gene Ontology — uses ChEBI terms to specify chemical participants in GO annotations
- PubChem — complementary chemical database with broader scope including non-biological compounds