Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Jan 4;44(D1):D1214-9.
doi: 10.1093/nar/gkv1031. Epub 2015 Oct 13.

ChEBI in 2016: Improved services and an expanding collection of metabolites

Janna Hastings  1 , Gareth Owen  2 , Adriano Dekker  2 , Marcus Ennis  2 , Namrata Kale  2 , Venkatesh Muthukrishnan  2 , Steve Turner  2 , Neil Swainston  3 , Pedro Mendes  3 , Christoph Steinbeck  4
Affiliations

ChEBI in 2016: Improved services and an expanding collection of metabolites

Janna Hastings et al. Nucleic Acids Res. .

Abstract

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.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
The organisation of a subset of the metabolite ontology classification in ChEBI, illustrating the hierarchical (‘is a’) classification of different types of metabolite, including those which have been significant in our curation efforts such as E.coli and human metabolite.
Figure 2.
Figure 2.
A screenshot of the new ChEBI advanced search page interface, showing the JavaScript structure sketcher Ketcher, and the new menu options along the top bar, which also includes a search box.
Figure 3.
Figure 3.
A screenshot of the result of plain enrichment analysis in BiNChE with the ChEBI structure ontology. The interface is draggable and zoomable. The intensity of the colour indicates the significance of the enrichment at each node.
Figure 4.
Figure 4.
A screenshot of a sample query and result page from the OntoQuery tool.
See this image and copyright information in PMC

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. de Matos P., Alcántara R., Dekker A., Ennis M., Hastings J., Haug K., Spiteri I., Turner S., Steinbeck C. Chemical Entities of Biological Interest: an update. Nucleic Acids Res. 2010;38:D249–D254. - PMC - PubMed
    1. Hastings J., de Matos P., Dekker A., Ennis M., Harsha B., Kale N., Muthukrishnan V., Owen G., Turner S., Williams M., et al. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 2013;41:D456–D63. - PMC - PubMed
    1. The UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 2015;43:D204–D212. - PMC - PubMed
    1. Herrgård M.J., Swainston N., Dobson P., Dunn W.B., Arga K.Y., Arvas M., Blüthgen N., Borger S., Costenoble R., Heinemann M., et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat. Biotechnol. 2008;26:1115–1160. - PMC - PubMed

Publication types

LinkOut - more resources