Digitalization and digital health are transforming research practices, while economic growth is increasingly driven by the information commons. In the case of biological sciences, information commons, such as public biobanks and free/libre open source software (FLOSS), are of paramount importance for both research and the bioeconomy. In a time of digitalization, however, information commons are vulnerable to violations, such as the free-rider problem, that render the commons unsustainable. Consequently, it has been argued that the enclosure of the informational common resources is the only means to effectively exploit them. Given the social and economic importance of the information commons, the new digital environment in biology and health requires governance innovation that will regulate the social embedding of the commons and their relationship to the free market, that is, a new political economy is needed. In this context, the need for a core common infrastructure, stretching from the physical to the logical and content layer of the information environment, that will guarantee the protection of the commons from both violations and enclosures, has been highlighted. Focusing on the interaction between two biological/bioinformatics commons, namely public biobanks and the FLOSS, we have set up an ecosystem relying on a blockchain technology. The proposed governance mechanism protects the information commons from the free-rider problem and guarantees their sustainability without hampering their operational framework. Our model demonstrates the interdependence and protection of the information commons not as an abstract theoretical exercise, but rather as a physical reality on the digital ontological matrix.