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Currently, in Nutritional Genomics it is crucial to have computing models and solutions and technological platforms in order to support acquisition, storage, management and presentation of all the information generated. Our aim is to build a biomedical ontology in order to formalise and integrate genomic, environmental and phenotypic data applied to Nutritional Genomics research focused on cardiovascular diseases and related phenotypes. Four different food composition tables have been employed to estimate the amount of nutrients provided by the diet. Web engineering technologies have been applied for constructing the Web platform containing the ontology, which integrates three distinct ontologies offering the corresponding models and services: food composition table alignment, gene-environment interaction, and cardiovascular risk estimation.