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.
Highlights
ChEBI is a database and ontology of chemical entities of biological interest containing a wide range of manually curated data items [1,2,3]
There are two main subontologies, namely a chemical entity ontology in which chemical entities are classified based on shared structural features, and a role ontology in which entities are classified based on their activities in biological or chemical systems or their use in applications
We describe two new tools that have been added to our online software suite, namely an analysis tool, BiNChE, and an ontology query tool, OntoQuery
Summary
ChEBI is a database and ontology of chemical entities of biological interest containing a wide range of manually curated data items [1,2,3]. Each entry in the database is assigned several metadata annotations, including where relevant a representation of the chemical structure, cross-references to other databases, multiple synonyms and alternative names in other languages, species in which a particular entity has been found and literature citations. ChEBI includes additional text from Wikipedia where possible (in turn, Wikipedia contains links back to ChEBI from their chemistry articles) and the monthly ‘Entity of the month’ article (http://www.ebi.ac.uk/chebi/ entityMonthForward.do) is a popular feature in which a particular entry in the database is highlighted in the context of a recent scientific discovery or appearance in the popular press.
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