The last several years have seen the emergence of digital libraries from which documents are harvested using the OAI-PMH protocol. Considering the volume of data provided by these repositories, we are interested in the exploitation of the full text content of scientific publications. Our aim is to bring new value to scientific publications by automatic extraction and semantic analysis. The identification of bibliographic references in texts makes it possible to localize specific text segments that carry linguistic markers in order to annotate a set of semantic categories related to citations. This work uses a categorization of surface linguistic markers organized in a linguistic ontology. The semantic annotations are used to enrich the document metadata and to provide new types of visualizations in an information retrieval context. We present the system architecture as well as some experimental results.