A major bottleneck for data-based policy making is that data sources are collected, managed, and distributed by different institutions, residing in different locations, resulting in conceptual and practical problems. The use of dispersed data for agricultural systems research requires the integration of data sources, which means to ensure consistency in data interpretations, units, spatial and temporal scales, to respect legal regulations of privacy, ownership and copyright, and to enable easy dissemination of data. This paper describes the SEAMLESS integrated database on European agricultural systems. It contains data on cropping patterns, production, farm structural data, soil and climate conditions, current agricultural management and policy information. To arrive at one integrated database, a shared ontology was developed according to a collaborative process, which facilitates interdisciplinary research. The paper details this process, which can be re-used in other research projects for integrating data sources.