The annotation of documents can be performed manually, semi-assisted or automated, also it can use the help of different knowledge resources as a set of rules or ontology. In this paper, we show the design of a semantic annotation tool that works automatically on power in order to efficiently manage academic documents in Spanish produced in the university related to computer science. The tool uses an ontology annotations to provide a corpus of documents the necessary attributes to be managed using other tools that use annotations as searchers or indexers. This is done by relating the concepts found in documents with concepts in the ontology performing semantic and syntactic comparisons, it is produced using open source tools for natural language processing and knowledge management.