The European Bioinformatics Institute has launched a freely available dictionary of 'small molecular entities'.
It’s all very well focusing on genes and the proteins they encode, say the curators of the service, but the purpose of most of those proteins is to interact with small molecules. The dictionary is designed to help researchers working on the role of proteins as transporters of, or facilitators of reactions between, small molecules.
The dictionary of Chemical Entities of Biological Interest (ChEBI) was launched in July and includes not only naturally occurring and synthetic small molecules but also atoms, ions, ion pairs and radicals. It will use nomenclature, symbolism and terminology endorsed by the International Union of Pure and Applied Chemistry (IUPAC) and the International Union of Biochemistry and Molecular Biology (IUBMB). Molecules directly encoded by the genome - nucleic acids, proteins and peptides derived from proteins by cleavage - will not generally be included.
Information on small molecular entities has been collected from three main sources: small molecules from the EBI’s IntEnz database of enzymes, the COMPOUND database from the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Chemical Ontology - a structured classification of chemical compounds of biological relevance.
Each entity in the database is described in terms of its chemistry and, where known, its broad biological function. Synonyms for each entity are also listed and are searchable.
’Until now there was no authoritative database of ’biochemical’ compounds in the public domain,’ says ChEBI coordinator Kirill Degtyarenko.
’This created problems because many biomedical databases need to refer to, or use data attached to, these small molecules.’