We present the interest of the Semantic Web techniques, particularly semantic annotation, in the biochip domain. We propose a semi-automatic method using the information extraction (IE) techniques for facilitating the generation of ontology-based annotations for scientific articles. Furthermore, we evaluate and discuss our method by applying it to the annotation of textual corpus provided by biologists working in the biochip domain. Finally, we argue that ontologybased semantic annotation can improve information retrieval.