Due to the increasing implementation of agile and networked manufacturing, supply chain has entered a new phase, virtual supply chain. The phase is characterized by the integration of activities, operations, and functions carried out at different and geographically distributed supply chain stages. The paper proposes an approach to the configuration of a network of small and medium-sized enterprises (SMEs) being integrated into a supply chain. The SME supply chain configuration is based on a shared domain ontology for supply chain management, offering the configuration task as a function of supply chain management. Principles of the development of the shared ontology and possible ways of matching between enterprise and domain ontologies are considered.