The ChEBI ontology

The ChEBI Ontology (1)

The ChEBI ontology is used to classify entities according to their structural and biological properties.

For biological properties, the relationship has_role is used. For example, diclofenac (CHEBI:47381; see Figure 8 below) has_role non-narcotic analgesic and has_role EC (prostaglandin-endoperoxide synthase) inhibitor.

Figure 8 Search results for diclofenac, showing the ChEBI ontology section.

For chemical properties, the is_a relationship is most commonly used (and it is the relationship which will be most familiar to ontologists), but a number of chemistry-specific relationships are also used, including:



is_conjugate_acid_of and is_conjugate_base_of

has_functional_parent and has_parent_hydride.

Thus diclofenac is_a  monocarboxylic acid, is_a secondary amino compound, and is_conjugate_acid_of diclofenac anion.

On the main display page for an entity, the chemical and biological roles and applications that are applicable to the entity are listed with the appropriate definitions immediately below the SMILES string for the entry. Beneath these, the immediate (one-step) structural links are shown. These are divided into two sections: 'Outgoing' (i.e. less specific terms) and 'Incoming' (i.e. more specific terms).

The ChEBI Ontology (2)

Full details about the ontological classification of an entity can be found by clicking on the 'ChEBI Ontology' tab, situated towards the top of the screen between the 'main' and 'Automatic Xrefs' tabs. Using this view, chemical and biological roles and applications are listed as on the Main display page, while both the names and structures of compounds linked by relationships such as 'is_enantiomer_of', 'is_tautomer_of' are displayed underneath. At the bottom of the page, is_a and has_part relationships are shown in a fully interactive graphical display (Figure 9).

Figure 9 Shows part of the ChEBI ontology tab for spermidine (CHEBI:16610).

Hovering the cursor over any line linking two terms in the graph will display the relationship between the terms (in this case, acetamides is_a monocarboxylic acid amide), while clicking on any name in the graph (in this case, acetamides) will display the definition of the term, together with a link which will take you to the ChEBI entry for that term.