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This paper presents an analysis of scientific collaboration through graph theory, based on a previous study focused on the collaborative work of researchers within an institution. This proposal also exposes the representation of inter-institutional collaboration of research groups, combining graph theory and data mining. The state of the art relates the concepts of scientific production, digital repositories, interoperability between repositories, the law of Open Science in Mexico, the theory of graphs and their use in previous studies for the analysis of scientific collaboration, and the definition of research groups in Mexico. Furthermore, the methodology uses elements of knowledge extraction for data mining, involving recovery, processing and visualization. Results present the collaboration status at the Universidad Autónoma de Yucatán, internally and externally, by the research groups. Internally, 22 groups were found and each researcher collaborates with six other professors within the institution, on average. In addition, consolidated research groups are those with the highest level of production and collaboration at national and international level, compared to the groups with less consolidation.