The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

Abstract

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.

Figure 1.

CHEBI:65460 is an example of a natural product recently introduced into ChEBI. It has been isolated from several different species, information about which is included in the new ‘Metabolite of Species’ section of the ChEBI web interface. The information about species and component is linked directly to the reference which acts as a source for that information.

Figure 2.

The newly introduced interactive graph-based ontology visualization shows paths from any ontology entity up to the root of the ontology. It supports two views: a compact view (the default, illustrated here) and an expanded view. In the compact view, paths traversing intervening entities for which no additional branching is introduced are suppressed (shown by a thicker line). These can be individually expanded by clicking on a thick line. The figure can be zoomed and any node can be dragged. Tooltips appear when a node is clicked on, giving the definition and other relevant information for that entity.

Figure 3.

In the expanded view of the interactive ontology visualization, all ancestor nodes and the immediate children of the selected entity are displayed. The other features of the display all remain unchanged.

Figure 4.

Inherited role classifications and chemical structural relationships are illustrated separately on the newly introduced ‘ChEBI Ontology’ tab, above the graph and tree view components. Where the entity being browsed is a role, the list of compounds having that role directly asserted or inherited is displayed in this section, showing the structures of the members and allowing navigation through large results by scrolling.