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

Abstract Summary 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. Availability and implementation The server is freely available for academic use at: http://ci.smu.edu.cn/genclip3/. Supplementary information Supplementary data are available at Bioinformatics online.