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In Biomedicine, provision of high-quality knowledge in terms of terminologies and consistent cross-references is a cornerstone for information retrieval, information extraction, text mining and federation of data repositories. Since the late 90 s we have been building knowledge resources to support these tasks. Over the years, we have gathered valuable experience by running various applications and by discussing with our scientists from different areas. Based on this experience, we are currently enhancing the content of our terminologies as well as the conceptual structures to represent cross-references. In the biomedical domain, there are long standing efforts to formally conceive knowledge repositories. With the era of the Semantic Web, a limited number of frameworks have achieved acceptance in the community aiming at semantic interoperability. Inspired by the knowledge engineering approaches in biomedicine, we propose a unified conceptual model for knowledge representation and its implementation. Contrary to the widespread frameworks, our model excels in its modularity. In addition, our formal approach is designed to be compatible to the main biomedical frameworks so that content can be exchanged in both directions.