Entity annotation is a fundamental step for entity relation extraction, information visualization and semantic web creation. Using domain specific ontologies to annotate a dataset for exploring, analyzing and integrating the entities and relations within the corpus is an important step for further study of the data. In this paper, we present an ontology based entity annotation system to annotate entities in neuroscience documents. To improve the annotation performance, we propose an ontology entity expansion method based on web service and ontology structure. We evaluate the proposed entity annotation method on real data obtained from Elsevier's BrainNavigator. The results show that using web service and ontology structure to expand ontology entities can improve the annotation result.