Chemical Vocabularies and Ontologies for Bioinformatics

The diversity of objects and concepts in biological chemistry can be reflected in the number of ways used to describe an ‘elementary’ biochemical event such as enzymatic reaction. The terminology used in publications or biological databases is often a mixture of terms borrowed from widely different or even contradictory classifications. The ever-growing knowledge cannot be processed meaningfully (e.g. efficiently and correctly referenced in biological databases) without organisation, from controlled vocabularies to dictionaries and thesauri to taxonomies and formal ontologies. Ontology of some domain of knowledge is a controlled vocabulary of terms with defined logical relationships to each other. The unique types of relationships between terms have to be included in biochemical ontologies. The relevance of chemical thesauri and ontologies to bioinformatics is illustrated by current resources and projects at the European Bioinformatics Institute, such as IntEnz (Enzyme Nomenclature), COMe (the bioinorganic motif database) and the IUPHAR Receptor Database.