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. 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.

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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

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References

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