This article describes a data set to map and model research collaborations in German biotechnology. Underlying micro-data for firms and institutions in the biotech sector together with information on their research collaboration partners have been extracted from a commercial industry directory, the BIOCOM Year and Address book, for 2005 and 2009. The data have been processed and aggregated to the level of NUTS3 regions. This core data set has been linked to regional covariates which measure the regional endowment with biotech-related research capacities, sector-specific S&T policy support and the strength of a region׳s overall local innovation system. The full data set, which is attached to this article, offers applied researchers an alternative source of information for empirical analyses of knowledge flows in research networks and for studying their determinants. Potential fields of application include social network and regression analysis. First empirical results are reported in “Determining factors of interregional research collaboration in Germany׳s biotech network: Capacity, proximity, policy?” (Mitze and Strotebeck, 2018) and “Centrality and get-richer mechanisms in interregional knowledge networks” (Mitze and Strotebeck, 2018).