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In this data paper, we provide a global dataset of urban perimeters that has been built in order to study the evolving geography of scientific activity at city level across the world. The method developed for building these agglomerations associates the distribution of population density and the distance between geolocalized scientific publications (issued between 1999 and 2014), whose author’s addresses have been systematically geocoded. The location of scientific production is obtained by processing bibliographic data retrieved in the Web of Science Core Collection (Clarivate Analytics). In the first part of the article, we detail the geocoding stage of our methodology. Next, we discuss the importance of delineating homogeneous urban perimeters to study the world geography of science production and we detail the methodology used to build these perimeters (the clustering stage). After discussing the extent to which our work can be re-used and enriched, we used this dataset to capture the worldwide distribution of Cybergeo publications at the city level between 2015 and 2017.