In this paper we investigate the use of Semantic Web languages such as RDF and OWL in textual encoding and we discuss several advantages these tools could provide. Among these, we show how the overlapping markup encoding problem can be naturally solved as the graph structure of the RDF language is naturally suited for this purpose. Further advantages in using Semantic Web based technologies lie in the powerful query and reasoning facilities that are already available and successfully used in the Semantic Web. The distributed and resource centric nature of RDF also enables a novel cooperative annotation scenario, where different encoding "facets" of the same text can be naturally merged. We then suggest the basic structure for an encoding ontology and evaluate the simplicity by which a complex query can be solved either programmatically or using existing Semantic Web query languages.