sr4gn a species recognition software tool for gene normalizationsr4gn物种基因正常化的识别软件工具.pdfVIP

SR4GN: A Species Recognition Software Tool for Gene Normalization 1,2 2 1 Chih-Hsuan Wei , Hung-Yu Kao , Zhiyong Lu * 1 National Center for Biotechnology Information (NCBI), National Library of Medicine, Bethesda, Maryland, United States of America, 2 Department of Computer Science and Information Engineering, National Cheng Kung University, Taiwan, Republic of China Abstract As suggested in recent studies, species recognition and disambiguation is one of the most critical and challenging steps in many downstream text-mining applications such as the gene normalization task and protein-protein interaction extraction. We report SR4GN: an open source tool for species recognition and disambiguation in biomedical text. In addition to the species detection function in existing tools, SR4GN is optimized for the Gene Normalization task. As such it is developed to link detected species with corresponding gene mentions in a document. SR4GN achieves 85.42% in accuracy and compares favorably to the other state-of-the-art techniques in benchmark experiments. Finally, SR4GN is implemented as a standalone software tool, thus making it convenient and robust for use in many text-mining applications. SR4GN can be downloaded at: /CBBresearch/Lu/downloads/SR4GN Citation: Wei C-H, Kao H-Y, Lu Z (2012) SR4GN: A Species Recognition Software Tool for Gene Normalization. PLoS ONE 7(6): e38460. doi:10.1371/ journal.pone.0038460 Editor: Jan Aerts, Leuven University, Belgium Received November 23, 2011; Accepted May 5, 2012; Published June 5, 2012 This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Funding: