Affiliations: National Institute of Informatics, Tokyo, Japan | National Institute of Infectious Diseases, Tokyo, Japan | Ochanomizu University, Tokyo, Japan | Centre for Comparative Genomics, Murdoch University, Perth, WA, Australia
Note:  Corresponding author: Ai Kawazoe, National Institute of Informatics, Hitotsubashi 2-1-2, Chiyoda-ku Tokyo 101-8430, Japan. Tel.: +81 3 4212 2536; Fax: +81 3 4212 2536; E-mail: [email protected]
Abstract: In this paper, we will report annotation experiments which show the advantage of applying a formal ontological methodology for constructing a schema for semantic annotation to mark up terms in the public health domain. We demonstrate that (1) a traditional task-oriented approach with a simple schema can cause several critical problems, and (2) the performance of annotators and the quality of annotated corpus is improved by applying formal ontological methodology in analyzing ‘markable’ categories of concepts and restructuring the schema. These results show that disciplined methods are useful for controlling the development of even quite modest semantic structures like annotation schema for entity recognition. We also report philosophical/logical considerations and decisions we made when we adopted the formal approach.
Keywords: Semantic annotation, ontology, named entity recognition, meta-property, text mining