What is ChEBI?


ChEBI scope and contents

ChEBI, EMBL-EBI’s database of Chemical Entities of Biological Interest, is a freely available, manually annotated database of small molecular entities  (molecules not encoded by the genome, Figure 1). These could include any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, or anything else that is a separately distinguishable entity.

ChEBI focuses on chemical nomenclature and structures, and provides a wide range of related chemical data such as formulae, links to other databases and an ontology for the chemical space. It aims to bridge the gap between small molecules and the macromolecules with which they interact in living systems.

Figure 1 ChEBI – an electronic 'dictionary' of chemistry terms for biologists.

What data can I find in ChEBI?

The ChEBI database combines chemical nomenclature, structures, synonyms and related chemical information from a number of freely accessible sources. All data are manually annotated to a high standard before public release, using nomenclature, symbolism and terminology endorsed by the International Union of Pure and Applied Chemistry (IUPAC) and the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB).

A major feature of ChEBI is that entries are related to each other using the ChEBI ontology. This represents the meaning of the data in a structured manner by creating relationships between entities and their parents (less specialised terms) and/or children (more specialised terms). ChEBI is probably the only chemistry database to include an ontology. The ChEBI ontology is used by a number of biological ontologies to manage their chemistry-related terms. For more information, see 'The ChEBI ontology' section of this Quick tour.

Data in ChEBI are divided into:

  1. Fully annotated (‘three star’) entries.
  2. Data curated elsewhere but not yet checked by ChEBI curators.

You can choose to search for 'three star' entries only, or to search 'All in ChEBI' (three star entries plus data curated elsewhere, Figure 2).

Figure 2 The text search box on the ChEBI home page, showing data status search options.