Ontologies in Metabolomics

Metabolomics studies the structure, function and relationships between biological and chemical entities. As we move toward systems biology we need to be certain that we are representing this knowledge consistently between studies and between laboratories. The application of ontology to metabolomics can improve the consistency of study data and can help link data using relationships that extend the computational capacity of the study data and enrich that knowledge source with a myriad of nationally available data to help fuel hypothesis driven laboratory based research.

Ontologies have been successfully used to map databases to each other so that they may be used more effectively. There are several databases used in metabolomics research,including general databases such as KEGG LIGAND, which contains information about chemical compounds, reactions, and enzymes relevant to life, and MetaCyc, a database of metabolic pathways; and organism-specific databases such as those for E. coli : the E. coli metabolome database (ECMDB) and EcoCyc. Some of these databases (namely, MetaCyc and EcoCyc) also have ontological components.