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Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

ChEBI encompasses an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified.

ChEBI uses nomenclature, symbolism and terminology endorsed by the following international scientific bodies:

Molecules directly encoded by the genome (e.g. nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI.

All data in the database is non-proprietary or is derived from a non-proprietary source. It is thus freely accessible and available to anyone. In addition, each data item is fully traceable and explicitly referenced to the original source.

Entity of the month

Image30 August 2006, 19-Norandrosterone 19-Norandrosterone (CHEBI:36412) is a naturally produced steroid and a metabolite of the anabolic steroid nandrolone, which is still used illegally by some athletes to boost muscle mass. Evidence for nandrolone abuse is normally provided from analysis of urine samples for 19-norandrosterone, although current tests are unable to distinguish whether the norandrosterone is of synthetic or physiological origin (it is produced naturally in the adrenal glands, gonads and placenta). Researchers at the German Sport University Cologne and the Montreal Anti-doping Laboratory at the INRS-Institut Armand-Frappier have recently developed a technique called gas chromatography combustion isotope ratio mass spectrometry, which can distinguish between the two by analysing the ratio of 13C to 12C in the urine samples. The method can detect concentrations of 19-norandrosterone as low as 2 ng per ml of urine (the level currently allowed by the World Anti-Doping Agency) and may help to resolve cases where athletes have elevated levels of 19-norandrosterone in their urine but insist that they have never taken steroids [Hebestreit et al. (2006) Analyst 131, 1021-1026].

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Current Status

The breakdown of the information available in ChEBI can be seen below.

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Sources

In order to create ChEBI, data from a number of sources were incorporated and subjected to merging procedures to eliminate redundancy. No data from external sources have been in any way altered but the data have been enriched by information from manual annotation.

Two of the main sources from which the data are drawn are:

  • IntEnz – the Integrated relational Enzyme database of the EBI. IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions.

  • KEGG COMPOUND – One part of the Kyoto Encyclopedia of Genes and Genomes LIGAND database, COMPOUND is a collection of biochemical compound structures.

Other data sources are listed in the User Manual

Data

ChEBI shows the following data fields:

  • ChEBI identifer – the unique identifer

  • ChEBI name – the name recommended for use in biological databases

  • ChEBI ASCII name – the ChEBI name with any special characters rendered in ASCII format

  • Structure – graphical representation(s) of a molecular structure and associated molfile(s), IUPAC International Chemical Identifier (InChI) and SMILES strings

  • Formula – Molecular formula

  • ChEBI Ontology

    • Parents and children
    • An option of a tree view of the position of the entry within the ChEBI Ontology

  • IUPAC name – name(s) generated according to recommendations of IUPAC

  • Synonyms – other names together with an indication of their source

  • Database links – manually curated cross-references to other non-proprietary databases

  • Registry number – CAS Registry Number, Beilstein Registry Number, Gmelin Registry Number (if available)

In addition a link is supplied to an entity's citations in UniProt (Universal Protein Resource), the central repository of protein sequence and function data contained in Swiss-Prot, TrEMBL, and PIR.

Acknowledgements

ImageChEBI is funded by the European Commission under FELICS, contract number 021902 (RII3) within the Research Infrastructure Action of the FP6 "Structuring the European Research Area" Programme.

In addition we would like to acknowledge the following software support.
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