This article introduces the concept of Networked Self-Developing Education System (NSDES). Such a system could be considered a modern university with a triple network structure where network team interactions between representatives of science, education and production are developed. A new model to explain NSDES intellectual capital development management is described. The model includes four interrelated parts (intellectual property, human, organisation and consumer types of capital). An important NSDES function is to provide conditions for lifelong self-development of scholars and students’ mastery of the scientific method. This is especially important for interdisciplinary natural sciences (biophysics, etc.). The NSDES has its integrative resource potential to meet this challenge. Such potential is accumulated in the open knowledge base and can be transferred to the education process provided knowledge is standardised in an ontology format. To build a course ontology to study the bioluminescent enzyme technology, the experience of developing ontology-based education solutions for railway universities which are evolving into “knowledge factories” is useful. Thus, “ontologisation” is proved to be a trend in the digital transformation of NSDES. The model’s implementation through ontology-based education solutions will create a foundation for the development of students’ research competences to solve urgent problems in sciences and industries.