Patient registries are a source of standardized electronic patient information. These records are vital to identify and coordinate a proper cohort, especially for the rare disease domain. Likeness, biobanks are currently an essential instrument for biomedical research, since they provide the very first piece of the biomedical research cycle, i.e. the biological samples. However, connection between rare diseases, patient registries and biobanks has been very limited, due to the lack of common data models and procedures. As they were built with security and privacy in mind, available tools lack comprehensive data access mechanisms, thus making data sharing a complex process. To tackle these challenges, we introduce a semantic web-based architecture to connect distributed and heterogeneous registries and samples. The outcome is a unique knowledge layer, connecting miscellaneous datasets and enabling state-of-the-art semantic data sharing mechanisms.