ChEBI

What kind of data does this resource provide ?

ChEBI (Chemical Entities of Biological Interest) is a freely available database and ontology of chemical entities focused on ‘small’ chemical compounds of biological significance. It covers a wide range of entities, including subatomic particles, atoms, chemical compounds, and ions. ChEBI provides detailed information on each entity, including a chemical structure, formula, mass, charge, structural identifiers such as InChI and SMILES, chemical ontology, chemical names, cross-references to other databases, and relevant literature citations.

Give me an example of the impact of this resource

ChEBI is widely used as a small molecule reference database by multiple biological databases worldwide. For many of these data resources, ChEBI is the sole source of accurate small molecule structural information linked to a unique and stable identifier. ChEBI uses an ontological structure to organise entities and establish relationships between entities.  Its ontology is semantically integrated with over 100 biomedical ontologies, thus providing powerful capabilities for data integration, hypothesis generation and reasoning.

ChEBI is extensively cross-linked to multiple data resources such as Gene Ontology, PDBe, UniProt, MetaboLights, IEDB, ChEMBL, Reactome, Rhea, BioModels, Europe PMC, and many more, enabling users to find additional information about a particular entity. Having such a widely used standard representation for small molecule data helps drive the data integration that is critical to contemporary AI and machine learning methods. Several data-driven companies make extensive use of ChEBI for various commercial applications including named entity recognition (NER), knowledge graphs and metadata management.

There have also been a number of tool developments utilising ChEBI’s data, such as the ChEBI corpus, CRAFT corpus, and Chebifier  ̶  a web tool for the automated classification of chemicals. Several groups have also used ChEBI to facilitate scientific methodologies  ̶  for example, in the development of a new prediction method for the identification of chemical toxicities, based on ChEBI’s ontology (as reported in Computational and Mathematical Methods in Medicine).

Key Facts

• The ChEBI database was established in 2004. It was developed, and is hosted, by the European Bioinformatics Institute (EBI) as part of the European Molecular Biology Laboratory (EMBL).
• ChEBI is one of the largest and most widely used ontologies in the chemical domain.
• ChEBI contains more than 198,000 entries, including both organic and inorganic compounds.

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