Infectious disease outbreaks such as the coronavirus disease 2019 (COVID-19) pandemic are reoccurring events, which require strong university research structures in the form of independent academic chairs. In Germany, however, inadequate research structures have been reported in various pandemic-relevant specialist areas over the last 30 years. Therefore, pandemic related topics (PARETO) was created as a unique, standardized and comparable evaluation platform to enable precise research funding. In this study protocol, the methods and analysis of PARETO are presented using the example of forensic medicine in the federal state of Saxony-Anhalt. First, a university department and reference department are selected to be analyzed and compared. The number of independent chairs at publicly funded medical faculties and university hospitals in 2021 is researched. Bibliometric data from the Web of Science are collected by choosing suitable Web of Science categories for the time period 1990–2021 (number of articles, number of citations, citation rate). They represent the research activity of the country, the federal states and the universities as well as important collaborations between institutions and countries. The data analysis is comparative and descriptive. Insights into the representation of pandemic-relevant departments in Germany can be expected, which will be demonstrated by the example of the study of forensic medicine. The evaluation platform created can serve decision-makers in politics and science to identify research funding needs and optimize research structures for future disease outbreaks.