Automatic extraction of HLA-disease interaction information from biomedical literature

JeongMin Chae, JiEun Chae, Taemin Lee, Younghee Jung, Heungbum Oh, Soon Young Jung

Research output: Chapter in Book/Report/Conference proceedingConference contribution


The HLA control a variety of function involved in immune response and influence susceptibility to over 40 diseases. It is important to find out how HLA cause the disease or modify susceptibility or course of it. In this paper, we developed an automatic HLA-disease information extraction procedure that uses biomedical publications. First, HLA and diseases are recognized in the literature using built-in regular languages and disease categories of Mesh. Second, we generated parse trees for each sentence in PubMed using collins parser. Third, we build our own information extraction algorithm. The algorithm searched parsing trees and extracted relation information from sentences. We automatically collected 10,184 sentences from 66,785 PubMed abstracts using HaDextract. The precision rate of extracted relations reported 89.6% in randomly selected 144 sentences.

Original languageEnglish
Title of host publicationCommunications in Computer and Information Science
Number of pages12
Publication statusPublished - 2009 Dec 1

Publication series

NameCommunications in Computer and Information Science
ISSN (Print)18650929



  • Disease
  • HLA
  • Interaction information
  • Textmining

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Chae, J., Chae, J., Lee, T., Jung, Y., Oh, H., & Jung, S. Y. (2009). Automatic extraction of HLA-disease interaction information from biomedical literature. In Communications in Computer and Information Science (Vol. 28, pp. 219-230). (Communications in Computer and Information Science; Vol. 28).