Semantic technologies are recognized as crucial in those domains, which intensively exploit information and communication technologies (ICT) and automation technologies (AT). Ontology engineering means can facilitate new functionalities, organizational structures and processes. Intra- and inter-organizational integration of different layers, functions, domains and processes may be simplified or enabled. Knowledge-driven solutions can be also facilitated. This paper investigates functional aspects of ontology-aided manufacturing and supply chain management by a literature review. The purpose is to assess potential for further research and to suggest its future key directions, aiming at novel solutions in terms of structures, controls, processes and functionalities.