Design of a multidisciplinary project is a complicated process requiring cooperation of different designers specialized in particular branches of engineering. The paper proposes a holonic approach to testify that a solution of distributed control systems is compliant with dynamically changing technology rules with ontology-based decomposition. The proposed holarchy includes a multi-agent system considering also its hybrid control architecture connected with a self-organization database. The proposed approach was implemented for a biotechnological pilot-plant continuously working as a platform for several process investigations.