Cognitive robots, able to adapt their actions based on sensory information and the management of uncertainty, have begun to find their way into manufacturing settings. However, the full potential of these robots has not been fully exploited, largely due to the lack of vertical integration with existing IT infrastructures, such as the manufacturing execution system (MES), as part of a large-scale cyber-physical entity. This paper reports on considerations and findings from the research project STAMINA that is developing such a cognitive cyber-physical system and applying it to a concrete and well-known use case from the automotive industry. Our approach allows manufacturing tasks to be performed without human intervention, even if the available description of the environment-the world model-suffers from large uncertainties. Thus, the robot becomes an integral part of the MES, resulting in a highly flexible overall system.