The first step retrieved and combined data on the metabolic reactants and their related products from three pathway databases, based on the harmonized RDF format. This data included the type of chemical relationship between the reaction pair using controlled vocabularies defined as ontologies. Additional recorded information was the pathway in which a reaction takes place, the enzyme which catalyzes the conversion, and literature references for pathways, reactions, metabolites, and proteins. Last, pathway and disease ontologies were retrieved.