RIscoper: a tool for RNA-RNA interaction extraction from the literature

Yang Zhang; Tianyuan Liu; Liqun Chen; Jinxurong Yang; Jiayi Yin; Yuncong Zhang; Zhixi Yun; Hao Xu; Lin Ning; Fengbiao Guo; Yongshuai Jiang; Hao Lin; Dong Wang; Yan Huang; Jian Huang

doi:10.1093/bioinformatics/btz044

RIscoper: a tool for RNA-RNA interaction extraction from the literature

Bioinformatics. 2019 Sep 1;35(17):3199-3202. doi: 10.1093/bioinformatics/btz044.

Authors

Yang Zhang¹, Tianyuan Liu², Liqun Chen², Jinxurong Yang², Jiayi Yin¹, Yuncong Zhang², Zhixi Yun¹, Hao Xu¹, Lin Ning¹, Fengbiao Guo¹, Yongshuai Jiang², Hao Lin¹, Dong Wang^{1

2

3}, Yan Huang^{2

3}, Jian Huang¹

Affiliations

¹ Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
² College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
³ Department of Bioinformatics, School of Basic Medical Science, Southern Medical University, Guangzhou, China.

PMID: 30668649
DOI: 10.1093/bioinformatics/btz044

Abstract

Motivation: Numerous experimental and computational studies in the biomedical literature have provided considerable amounts of data on diverse RNA-RNA interactions (RRIs). However, few text mining systems for RRIs information extraction are available.

Results: RNA Interactome Scoper (RIscoper) represents the first tool for full-scale RNA interactome scanning and was developed for extracting RRIs from the literature based on the N-gram model. Notably, a reliable RRI corpus was integrated in RIscoper, and more than 13 300 manually curated sentences with RRI information were recruited. RIscoper allows users to upload full texts or abstracts, and provides an online search tool that is connected with PubMed (PMID and keyword input), and these capabilities are useful for biologists. RIscoper has a strong performance (90.4% precision and 93.9% recall), integrates natural language processing techniques and has a reliable RRI corpus.

Availability and implementation: The standalone software and web server of RIscoper are freely available at www.rna-society.org/riscoper/.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Data Mining
PubMed
Publications
RNA
Software*

Substances

RNA