The ultimate goal in the pharmaceutical sector is product quality. However this quality can be altered by the use of a number of heterogeneous information systems with different business structures and concepts along the lifecycle of the product. Interoperability is then needed to guarantee a certain correspondence and compliance between different product data. In this paper we focus on a particular compliance problem, between production technical data, represented in an ERP, and the corresponding regulatory directives and specifications, represented by the Marketing Authorizations (MA). The MA detail the process for manufacturing the medicine according to the requirements imposed by health organisations such as Food and Drug Administration (FDA) and Committee for Medicinal Products for Human use (CHMP). The proposed approach uses an interoperability framework which is based on a multi-layer separation between the organisational aspects, business trades, and information technologies for each involved entity into the communication between the used systems.