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ChEBI - Chemical Entities of Biological Interest


NAR Molecular Biology Database Collection entry number 646
de Matos P.1, Ennis M.1, Zbinden M.1, McNaught A.1, Alcántara R.1, Darsow M.1, Guedj M.1,2, Ashburner M.3 and Degtyarenko K.1
1EMBL Outstation - The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
2Laboratoire Statistique et Génome, Université d'Evry Val d'Essonne, France
3Department of Genetics, University of Cambridge, Cambridge, UK

Database Description

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity [1]. 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 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:- International Union of Pure and Applied Chemistry (http://www.iupac.org/) (IUPAC)
- Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (http://www.iubmb.org/) (NC-IUBMB)
All data in the database is non-proprietary or is derived from a non-proprietary source. Each data item is fully traceable and explicitly referenced to the original source.

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
- Definition - a short verbal definition is included in some entries, especially relevant to classes
- Structure - graphical representation(s) of a molecular structure and associated molfile(s), IUPAC International Chemical Identifier (InChI) and SMILES strings
- Formula - Molecular formula
- Parents and children, according to ChEBI Ontology
- IUPAC name - a name generated according to the 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 numbers - CAS Registry Number, Beilstein Registry Number, Gmelin Registry Number (if available)
- Comment(s) - A free-text comment may be added to some terms, especially in cases where confusing terminology has been historically used. A comment may relate to a single term or to the entry as a whole.
The ChEBI terms have been automatically mapped to the UniProt (http://www.ebi.uniprot.org/) database, and for each ChEBI entity the list of UniProt entries containing the relevant terms are available. ChEBI can be accessed through the WWW (http://www.ebi.ac.uk/chebi/) or may be downloaded by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/chebi/).

Recent Developments

Structures: ChEBI stores two- or three-dimensional structural diagrams as connection tables in MDL molfile format. One entity can have one or more connection tables. The diagrams are shown as the static images or can be visualised with an interactive MarvinView applet (http://www.chemaxon.com/marvin/). The IUPAC International Chemical Identifier (InChI?; http://www.iupac.org/inchi/) and SMILES (http://www.daylight.com/smiles/) strings are generated for the corresponding molecules.
ChEBI Ontology consists of four sub-ontologies:
- Molecular Structure, in which molecular entities or parts thereof are classified according to structure;
- Biological Role, which classifies entities on the basis of their role within a biological context (e.g. antibiotic, coenzyme, hormone);
- Application, which classifies entities, where appropriate, on the basis of their intended use by humans (e.g. pesticide, drug, fuel);
- Subatomic Particle, which classifies particles smaller than atoms.
The ontology uses the following relationship types:
is a
is part of
is conjugate acid of and is conjugate base of
is tautomer of
is enantiomer of
has functional parent
has parent hydride
is substituent group from
Web Services: the main aim of ChEBI Web Services (http://www.ebi.ac.uk/chebi/webServices.do) is to provide programmatic access to the ChEBI database in order to aid our users in integrating ChEBI into their applications. ChEBI provides Simple Object Access Protocol (SOAP) access to its database. Both Java and perl clients are available through which you can access the data.To obtain ‘lightweight’ ontology objects, the Ontology Lookup Service (http://www.ebi.ac.uk/ontology-lookup/) [2] can be used as alternative Web Services.
SourceForge forum (http://sourceforge.net/projects/chebi/) has been established and is used to report bugs, discuss annotation issues and to request the new ChEBI terms or entries.
PubChem deposition: the structures of molecular entities from ChEBI are deposited to PubChem (http://pubchem.ncbi.nlm.nih.gov/)

Acknowledgements

The ChEBI project is supported by the European Commission under FELICS, contract number 021902 (RII3). We are also grateful to David Binns, Henning Hermjakob, Michael Kleen, Ernst Kretschmann, Mark Rijnbeek, Karine Robbe, Philippe Rocca-Serra and Daniela Wieser.

References

1. McNaught, A.D. and Wilkinson, A., Eds. (1997) Compendium of Chemical Terminology ("The Gold Book"), 2nd Edition. Blackwell Scientific Publications, Oxford, p. 262. 2. Cote, R.G., Jones, P., Apweiler, R., Hermjakob, H. (2006) The ontology lookup service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 7(1), 97.

Subcategory: Small molecules

Go to the abstract in the NAR 2010 Database Issue.
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