ChEBI

ChEBI
Content
Description Chemical database
Data types
captured		 Chemical Entities of Biological Interest
Contact
Research center European Molecular Biology Laboratory
Laboratory United Kingdom European Bioinformatics Institute
Primary citation [1]
Access
Website ChEBI
Download URL Downloads
Web service URL Web Service
Sparql endpoint BIO2RDF
Tools
Web ChEBI Website
Miscellaneous
Data release
frequency		 monthly
Curation policy Manually curated

Chemical Entities of Biological Interest, also known as ChEBI,[1][2] is a database and ontology of molecular entities focused on 'small' chemical compounds, that is part of the Open Biomedical Ontologies effort. 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".[3] The molecular entities in question are either products of nature or synthetic products which have potential bioactivity. Molecules directly encoded by the genome, such as nucleic acids, proteins and peptides derived from proteins by proteolytic cleavage, are not as a rule included in ChEBI.

ChEBI uses nomenclature, symbolism and terminology endorsed by the International Union of Pure and Applied Chemistry (IUPAC) and Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB).

Scope and access

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.

The ChEBI data is available through a public web interface, Web Service and downloads.

Similarity measures

Semantic similarity measures exploring the hierarchy of ChEBI classes[4] and its disjointness axioms[5] were shown to be a feasible and effective way to compare chemical compounds and improve classification systems.

See also

References

  1. 1 2 de Matos P, Alcántara R, Dekker A, Ennis M, Hastings J, Haug K, Spiteri I, Turner S, Steinbeck C (January 2010). "Chemical Entities of Biological Interest: an update". Nucleic Acids Research. 38 (Database issue): D249–54. doi:10.1093/nar/gkp886. PMC 2808869. PMID 19854951.
  2. ↑ Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M (January 2008). "ChEBI: a database and ontology for chemical entities of biological interest". Nucleic Acids Research. 36 (Database issue): D344–50. doi:10.1093/nar/gkm791. PMC 2238832. PMID 17932057.
  3. ↑ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version:  (2006–) "molecular entity".
  4. ↑ Ferreira JD, Couto FM (September 2010). "Semantic similarity for automatic classification of chemical compounds". PLoS Computational Biology. 6 (9). Bibcode:2010PLSCB...6E0937F. doi:10.1371/journal.pcbi.1000937. PMC 2944781. PMID 20885779.
  5. ↑ Ferreira JD, Hastings J, Couto FM (November 2013). "Exploiting disjointness axioms to improve semantic similarity measures". Bioinformatics. 29 (21): 2781–7. doi:10.1093/bioinformatics/btt491. PMID 24002110.
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