Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://www.ebi.ac.uk/chebi/
Full name: Chemical Entities of Biological Interest
Description: ChEBI is a database and ontology of chemical entities of biological interest. It is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
Year founded: 2008
Last update: 2019-4-1
Version: v135.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United Kingdom
Data type:
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: European Bioinformatics Institute
Address: Hinxton, CB10 1SD, UK
City: Cambridge
Province/State:
Country/Region: United Kingdom
Contact name (PI/Team): Janna Hastings
Contact email (PI/Helpdesk): hastings@ebi.ac.uk

Publications

26467479
ChEBI in 2016: Improved services and an expanding collection of metabolites. [PMID: 26467479]
Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C.

ChEBI is a database and ontology containing information about chemical entities of biological interest. It currently includes over 46 000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, synonyms and literature citations. All content is freely available and can be accessed online at http://www.ebi.ac.uk/chebi. In this update paper, we describe recent improvements and additions to the ChEBI offering. We have substantially extended our collection of endogenous metabolites for several organisms including human, mouse, Escherichia coli and yeast. Our front-end has also been reworked and updated, improving the user experience, removing our dependency on Java applets in favour of embedded JavaScript components and moving from a monthly release update to a 'live' website. Programmatic access has been improved by the introduction of a library, libChEBI, in Java, Python and Matlab. Furthermore, we have added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2016:44(D1) | 182 Citations (from Europe PMC, 2021-06-19)
23180789
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. [PMID: 23180789]
Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C.

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 in content, and has added several new features. In addition to incorporating all user-requested compounds, our annotation efforts have emphasized immunology, natural products and metabolites in many species. All database entries are now 'is_a' classified within the ontology, meaning that all of the chemicals are available to semantic reasoning tools that harness the classification hierarchy. We have completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology. Furthermore, we have aligned our chemical classification with the classification of chemical-involving processes in the Gene Ontology (GO), and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them. This effort necessitated incorporating many additional biologically relevant compounds. We have incorporated additional data types including reference citations, and the species and component for metabolites. Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization.

Nucleic Acids Res. 2013:41(Database issue) | 265 Citations (from Europe PMC, 2021-06-19)
19854951
Chemical Entities of Biological Interest: an update. [PMID: 19854951]
de Matos P, Alcántara R, Dekker A, Ennis M, Hastings J, Haug K, Spiteri I, Turner S, Steinbeck C.

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.

Nucleic Acids Res. 2010:38(Database issue) | 140 Citations (from Europe PMC, 2021-06-19)
19496059
ChEBI: an open bioinformatics and cheminformatics resource. [PMID: 19496059]
Degtyarenko K, Hastings J, de Matos P, Ennis M.

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on "small" chemical compounds. This unit provides a detailed guide to browsing, searching, downloading, and programmatic access to the ChEBI database.

Curr Protoc Bioinformatics. 2009:Chapter 14() | 5 Citations (from Europe PMC, 2021-06-19)
17932057
ChEBI: a database and ontology for chemical entities of biological interest. [PMID: 17932057]
Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M.

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/

Nucleic Acids Res. 2008:36(Database issue) | 344 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
132/5061 (97.412%)
Health and medicine:
28/1067 (97.47%)
Standard ontology and nomenclature:
12/204 (94.608%)
132
Total Rank
936
Citations
72
z-index

Community reviews

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Record metadata

Created on: 2015-06-20
Curated by:
Lina Ma [2019-04-16]
Pei Wang [2018-01-27]
Mengwei Li [2016-03-31]
Mengwei Li [2016-02-21]
lin liu [2016-02-02]
lin liu [2016-01-17]
Mengwei Li [2015-12-02]
Mengwei Li [2015-06-27]