The development of scientific subject domains ontologies is both challenging and demanding. Ontologies should not only represent a large number of concepts but also ensure their uniform and consistent description. This result is much easier to achieve if you build an ontology using ontology design patterns. These are intended to describe solutions to typical problems arising regularly when developing the ontologies of different subject domains. Ontology design patterns are intended to streamline and facilitate the process of building ontologies and help developers avoid the frequent repetitive errors of ontological modeling. The paper presents a methodology for building the ontologies of scientific subject domains, which offers a representative set of ontology design patterns and a method for their application. The patterns used in this methodology have appeared as a result of solving ontological modeling problems, which the authors of the paper encountered in the process of developing ontologies for various scientific subject domains.