Nowadays, the number of scientifc publications existing in the form of electronic text is constantly growing. As a result, the tasks related to the text processing of scientifc articles become especially actual. This paper is dedicated to the task of extracting semantic relations between entities from the texts of scientifc articles in Russian, where we consider scientifc terms as entities. Relation extraction can be useful in some specialized areas, such as searching and question-answering systems, as well as in the compilation of ontologies. In our work, we have created a corpus of scientifc texts consisting of 136 abstracts of scientifc articles in Russian, in which 353 relations of the following types were highlighted: USAGE, ISA, TOOL, SYNONYMS, PART_OF, CAUSE. This corpus was used to train the machine learning models. In addition, we have implemented the automatic semantic relation extraction algorithm and tested it on the already existing corpus RuSERRC. The neural network model BERT was used to implement the algorithm. We’ve done a number of experiments using vectors derived from different language models, as well as two neural network architectures. The developed tool and the annotated corpus are publicly available and can be useful for other researchers.