Over the last decade the biological sciences have been widely embracing Systems Biology and its various data integration approaches to discover new knowledge. Molecular Systems Biology aims to develop hypotheses based on integrated, or modelled data. These hypotheses can be subsequently used to design new experiments for testing, leading to an improved understanding of the biology; a more accurate model of the biological system and therefore an improved ability to develop hypotheses. During the same period the biosciences have also eagerly taken up the emerging Semantic Web as evidenced by the dedicated exploitation of semantic web technologies for data integration and sharing in the Life Sciences. We describe how these two approaches merged in Semantic Systems Biology: a data integration and analysis approach complementary to model-based Systems Biology. Semantic Systems Biology augments the integration and sharing of knowledge, and opens new avenues for computational support in quality checking and automated reasoning, and to develop new, testable hypotheses.