Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 36 (Database issue), D344-50

ChEBI: A Database and Ontology for Chemical Entities of Biological Interest

Affiliations

ChEBI: A Database and Ontology for Chemical Entities of Biological Interest

Kirill Degtyarenko et al. Nucleic Acids Res.

Abstract

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities. ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi/

Figures

Figure 1.
Figure 1.
Fragment of ChEBI Ontology.

Similar articles

  • Chemical Entities of Biological Interest: An Update
    P de Matos et al. Nucleic Acids Res 38 (Database issue), D249-54. PMID 19854951.
    Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The molecular entities in q …
  • The ChEBI Reference Database and Ontology for Biologically Relevant Chemistry: Enhancements for 2013
    J Hastings et al. Nucleic Acids Res 41 (Database issue), D456-63. PMID 23180789.
    ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. Over the past few years, ChEBI has continued to grow steadily i …
  • ChEBI: An Open Bioinformatics and Cheminformatics Resource
    K Degtyarenko et al. Curr Protoc Bioinformatics Chapter 14, Unit 14.9. PMID 19496059.
    Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on "small" chemical compounds. This unit provides a detail …
  • Using ZINC to Acquire a Virtual Screening Library
    JJ Irwin. Curr Protoc Bioinformatics Chapter 14, Unit 14.6. PMID 18551414. - Review
    The ZINC database of commercially available compounds contains biologically relevant representations of purchasable compounds in ready-to-screen formats. ZINC uses catalo …
  • Using ChemBank to Probe Chemical Biology
    K Petri Seiler et al. Curr Protoc Bioinformatics Chapter 14, Unit 14.5. PMID 18551413. - Review
    ChemBank (http://chembank.broad.harvard.edu/) is a public, Web-based informatics environment. ChemBank stores and makes freely available data derived from small molecules …
See all similar articles

Cited by 299 PubMed Central articles

See all "Cited by" articles

References

    1. Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, et al. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2006;34:D511–D516. - PMC - PubMed
    1. Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya S, Bower L, et al. EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res. 2007;35:D16–D20. - PMC - PubMed
    1. The UniProt Consortium. The Universal Protein Resource (UniProt) Nucleic Acids Res. 2007;35:D193–D197. - PMC - PubMed
    1. Weininger D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 1988;28:31–36.
    1. Degtyarenko K, Ennis M, Garavelli J. “Good annotation practice” for chemical data in biology. In Silico Biol. 2007;7:S1, 06. - PubMed

Publication types

Feedback