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

Jia-Hong Wang; Ling-Feng Zhao; Hua-Feng Wang; Yue-Ting Wen; Kui-Kui Jiang; Xiang-Ming Mao; Zi-Ying Zhou; Kai-Tai Yao; Qing-Shan Geng; Dan Guo; Zhong-Xi Huang

doi:10.1093/bioinformatics/btz807

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

Bioinformatics. 2019 Nov 4:btz807. doi: 10.1093/bioinformatics/btz807. Online ahead of print.

Authors

Affiliations

¹ Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R China.
² Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, P.R China.
³ Shunde Hospital, Southern Medical University, Foshan, P.R China.
⁴ Department of Medical Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, P. R. China.
⁵ Department of Urology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, P.R China.
⁶ Guangdong General Hospital, Guangzhou, China.
⁷ Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou, P.R China.

PMID: 31681951
DOI: 10.1093/bioinformatics/btz807

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: The server is freely available for academic use at: http://ci.smu.edu.cn/genclip3/.

Supplementary information: Supplementary data are available at Bioinformatics online.