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, 38 (Database issue), D249-54

Chemical Entities of Biological Interest: An Update

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Chemical Entities of Biological Interest: An Update

Paula de Matos 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/. This article reports on new features in ChEBI since the last NAR report in 2007, including substructure and similarity searching, a submission tool for authoring of ChEBI datasets by the community and a 30-fold increase in the number of chemical structures stored in ChEBI.

Figures

Figure 1.
Figure 1.
Illustrates the first step in the ChEBI Submission procedure allowing the user to input the chemical structure, name and definition.

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References

    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. - PMC - PubMed
    1. Dimitropoulos D, Ionides J, Henrick K. Using MSDchem to Search the PDB Ligand Dictionary. Curr. Protoc. Bioinform. 2006:14.3.1–14.3.21. - PubMed
    1. Batchelor C. An upper-level ontology for chemistry. In: Eschenbach C, Grüninger M, editors. Formal Ontology in Information Systems, Proceedings of the Fifth international Conference, FOIS 2008, Saarbrücken, October 31st – 3rd November 2008. Amsterdam: IOS Press; 2008. pp. 195–207.
    1. Smith B, Cuesters W, Klagges B, Köhler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C. Relations in Biomedical Ontologies. Genome Biol. 2005;6:R46. - PMC - PubMed
    1. Steinbeck C, Kuhn S. NMRShiftDB—compound identification and structure elucidation support through a free community-built web database. Phytochemistry. 2004;65:2711–2717. - PubMed

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