Breast cancer research need the development of specific and suitable tools to appropriately manage biomolecular knowledge. The presented work deals with the integrative storage of breast cancer related biological data, in order to promote a system biology approach to this network disease. To increase data standardization and resource integration, annotations maintained in Genes-to-Systems Breast Cancer (G2SBC) database are associated to ontological terms, which provide a hierarchical structure to organize data enabling more effective queries, statistical analysis and semantic web searching. Exploited ontologies, which cover all levels of the molecular environment, from genes to systems, are among the most known and widely used bioinformatics resources. In G2SBC database ontology terms both provide a semantic layer to improve data storage, accessibility and analysis and represent a user friendly instrument to identify relations among biological components.