The Resource Description Framework (RDF) is an interoperable data representation format suitable for interchange and integration of data, especially in Open Data contexts. However, RDF is also becoming increasingly attractive in scenarios involving sensitive data, where data protection is a major concern. At its core, RDF does not support any form of access control and current proposals for extending RDF with access control do not fit well with the RDF representation model. Considering an enterprise scenario, we present a modelling that caters for access control over the stored RDF data in an intuitive and transparent manner. For this paper we rely on Annotated RDF, which introduces concepts from Annotated Logic Programming into RDF. Based on this model of the access control annotation domain, we propose a mechanism to manage permissions via application-specific logic rules. Furthermore, we illustrate how our Annotated Query Language (AnQL) provides a secure way to query this access control annotated RDF data.