GenCLiP 3: mining human genes' functions and regulatory networks from PubMed based on co-occurrences and natural language processing.

Wang, Jia-Hong; Zhao, Ling-Feng; Wang, Hua-Feng; Wen, Yue-Ting; Jiang, Kui-Kui; Mao, Xiang-Ming; Zhou, Zi-Ying; Yao, Kai-Tai et al. · Bioinformatics · 2019

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Abstract

We present a web server, GenCLiP 3, which is an updated version of GenCLiP 2.0 to enhance analysis of human gene functions and regulatory networks, with the following improvements: i) accurate recognition of molecular interactions with polarity and directionality from the entire PubMed database; ii) support for Boolean search to customize multiple-term search and to quickly retrieve function related genes; iii) strengthened association between gene and keyword by a new scoring method; and iv) daily updates following literature release at PubMed FTP. The server is freely available for academic use at: http://ci.smu.edu.cn/genclip3/. Supplementary data are available at Bioinformatics online.