Introduction

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. RIscoper (RNA Interactome Scoper) 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.


Highlights

  • RIscoper is based on N-gram statistics language model tool for full-scale RNA interactome scanning, that supports users in the upload of full texts or abstracts and provides an online search tool connection with PubMed (PMID and keyword input).
  • RIscoper establishes a comprehensive and reliable RRI corpus that recruits 13,377 sentences with RRI information manually curated from more than 5,000 biomedical literatures. It provides a favorable resource for ongoing text mining studies of RRIs and represents a benchmark dataset for future machine learning works.
  • RIscoper is a simple and practical tool for database curators, experimental biologists and bioinformaticians.


News


  • RIscoper completed
    September 2018

  • RIscoper construction
    September 2017

  • Data collection
    April 2017




Contact


Wang Dong



wangdong@ems.hrbmu .edu.cn