In this work we propose to present an application that supports the representation of manuscript documents according to an ontological approach. The implementation of this application makes it possible to annotate semantically these manuscripts according to the ontology "OMOS" [1]. The semantic annotation proposed here is an annotation based on an ontology of the "OMOS" manuscripts of generation and use of specific metadata targeted to allow new methods of access to information and to extend existing ones. The proposed annotation is based on the understanding that the named entities (the author, date 'link ... etc.) mentioned in the documents constitute an important part of their semantics. Finally, this application gives us an annotation file associated with each document.