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With the rapid growth of articles of genomics research, it has become a challenge for biomedical researchers to access this ever-increasing quantity of information to understand the newest discovery of functions of proteins they are studying. To facilitate functional annotation of proteins by utilizing the huge amounts of biomedical literature and transforming the knowledge into easily accessible database formats, the text mining technique thus becomes essential. In this paper, we propose the method of sentence pattern mining to extract protein functions from biomedical literature. To recognize variants of function terms correctly, we identify morphological, syntactic, and semantic variation forms. The proposed methods can be used to aid database curators in annotating protein functions and to assist biologists and medical researchers in searching protein functions from biomedical literature.