The article discusses models and mechanisms of transdisciplinary research in the perspective of creating clusters of disciplinary convergence and scientific theories, formal representation of knowledge, and the formation of the knowledge industry using a unified ontology engineering devkit. Special attention is focused on the possibilities of research-related design for the creation of new knowledge and technologies. A conceptual analysis of ontology engineering is conducted, indicating the importance and effectiveness of applying ontology knowledge and mechanisms in solving user tasks. The domain ontology, its ontology graph, and their essential differences and advantages from owl ontologies are examined in depth. An example of the application of task ontology to the design of programmable microchip computing devices is proposed. Keywords: knowledge industry, ontology engineering, transdisciplinary research, convergence clusters, research-related design, new knowledge and technologies, domain ontology, ontology graph, task ontology.