Interpretation knowledge extraction for genetic testing via question-answer model.

Journal: BMC genomics
PMID: 39522019

Abstract

BACKGROUND: Sequencing-based genetic testing is widely used in biomedical research, including pathogenic microorganism detection with metagenomic next-generation sequencing (mNGS). The application of sequencing results to clinical diagnosis and treatment relies on various interpretation knowledge bases. Currently, the existing knowledge bases are primarily built through manual knowledge extraction. This method requires professionals to read extensive literature and extract relevant knowledge from it, which is time-consuming and costly. Furthermore, manual extraction unavoidably introduces subjective biases. In this study, we aimed to automatically extract knowledge for interpreting mNGS results.

Authors

  • Wenjun Wang
    College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing, China.
  • Huanxin Chen
    School of Software Engineering, South China University of Technology, Guangzhou, China.
  • Hui Wang
    Department of Vascular Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China.
  • Lin Fang
    BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.
  • Huan Wang
    Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai, P. R. China.
  • Yi Ding
    Clinical and Research Center of AIDS, Beijing Ditan Hospital, Capital Medical University, Beijing, China.
  • Yao Lu
    Department of Laboratory Medicine, The First Affiliated Hospital of Ningbo University, Ningbo First Hospital, Ningbo, China.
  • Qingyao Wu

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