One of the greatest challenges in creating effective decision-making systems for connected enterprises is the management of cross-domain information. In manufacturing value networks where supply chains are increasingly intertwined, and closed-loop lifecycle management requires traversing several domains, ontologies are proving to be a reliable reference for cross-domain semantic interoperability. However, ontology development, implementation, and management are fragmented and difficult for new users of ontologies to grasp. This is a significant challenge in environments where ontologies are vital for managing effective data exchanges in complex industrial processes. The OntoCommons project has evolved an ontology ecosystem that aims to lower the entry barrier to using ontologies. Building on this ambition, we present a holistic approach to the integration and management of ontologies horizontally across manufacturing ecosystems, including the creation of reference documentation for manufacturing value networks and related standards, available tools for working with ontologies, and examples of vertical integration of knowledge from application level with domain-level and top-level ontology reference documentation. As a novel research direction, we propose a meta-level approach to ontology-driven knowledge management in manufacturing ecosystems. Based on evidence from recent breakthroughs, we present future and emerging research directions.