Skip to main content
  • Poster presentation
  • Open access
  • Published:

ChEBI: a chemistry ontology and database

The bioinformatics community has developed a policy of open access and open data since its inception. This is contrary to chemoinformatics which has traditionally been a closed-access area. In 2004, two complementary open access databases were initiated by the bioinformatics community, ChEBI [1] and PubChem. PubChem serves as automated repository on the biological activities of small molecules and ChEBI (Chemical Entities of Biological Interest) as a manually annotated database of molecular entities focused on 'small' chemical compounds. Although ChEBI is reasonably compact containing just over 18,000 entities, it provides a wide range of data items such as chemical nomenclature, an ontology and chemical structures. The ChEBI database has a strong focus on quality with exceptional efforts afforded to IUPAC nomenclature rules, classification within the ontology and best IUPAC practices when drawing chemical structures.

ChEBI is currently undergoing a period of restructuring which will allow it to incorporate the small molecule structures from (and link to) EBI's new chemogenomics database ChEMBL [2], increasing its small molecules coverage to over 500,000 entities. We have restructured the chemical structure search facility to use Orchem [3] an Oracle chemistry plug-in using the Chemistry Development Kit [4]. The facility allows a user to draw a chemical structure or load one from a file and then execute either a substructure or similarity search. Furthermore the ChEBI text search will have extensive facilities for querying based on not only names but formula, a range of charges and molecular weight. The ability to query the ChEBI ontology and retrieve all children for a given entity will also be included.

In order to aid the distribution of ChEBI to the chemoinformatics community we have extended our export formats to include an MDL sdf format with a lighter version consisting only of compound structure, name and identifier. A complete version is available with all the ChEBI data properties such as synonyms, cross-references, SMILES and InChI. Furthermore cross-references in ChEBI have been extended to include BRENDA the enzyme database, NMRShiftDB the database for organic structures and their nuclear magnetic resonance (nmr) spectra, Rhea the biochemical reaction database and IntEnz the enzyme nomenclature database.

ChEBI is available at


  1. Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M: ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 2008, 36: D344-D350. 10.1093/nar/gkm791.

    Article  CAS  Google Scholar 

  2. []

  3. Rijnbeek M, Steinbeck C: An open source chemistry search engine for Oracle.

  4. Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Willighagen EL: The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. J Chem Inf Comput Sci. 2003, 43 (2): 493-500.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations


Rights and permissions

Open Access This is an open access article distributed under the terms of the Creative Commons Attribution Noncommercial License ( ), which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.

Reprints and permissions

About this article

Cite this article

de Matos, P., Dekker, A., Ennis, M. et al. ChEBI: a chemistry ontology and database. J Cheminform 2 (Suppl 1), P6 (2010).

Download citation

  • Published:

  • DOI: