The administration of electronic publication in the Information Era congregates old and new problems, especially those related with Information Retrieval and Automatic Knowledge Extraction. This article presents an Information Retrieval System that uses Natural Language Processing and Ontology to index collection’s texts. We describe a system that constructs a domain specific ontology, starting from the syntactic and semantic analyses of the texts that compose the collection. First the texts are tokenized, then a robust syntactic analysis is made, subsequently the semantic analysis is accomplished in conformity with a metalanguage of knowledge representation, based on a basic ontology composed of 47 classes. The ontology, automatically extracted, generates richer domain specific knowledge. It propitiates, through its semantic net, the right conditions for the user to find with larger efficiency and agility the terms adapted for the consultation to the texts. A prototype of this system was built and used for the indexation of a collection of 221 electronic texts of Information Science written in Portuguese from Brazil. Instead of being based in statistical theories, we propose a robust Information Retrieval System that uses cognitive theories, allowing a larger efficiency in the answer to the users’ queries.