Automatic extraction of HLA-disease interaction information from biomedical literature

Jeong Min Chae; Ji Eun Chae; Taemin Lee; Younghee Jung; Heungbum Oh; Soonyoung Jung

doi:10.1007/978-3-642-10238-7_18

Automatic extraction of HLA-disease interaction information from biomedical literature

Jeong Min Chae, Ji Eun Chae, Taemin Lee, Younghee Jung, Heungbum Oh, Soonyoung Jung

Department of Computer Science and Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

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 language	English
Title of host publication	Advances in Computational Science and Engineering
Subtitle of host publication	Second International Conference, FGCN 2008, Workshops and Symposia, Sanya, Hainan Island, China, December 13-15, 2008. Revised Selected Papers
Editors	Tai-hoon Kim, Laurence T. Yang, Jong Hyuk Park, Alan Chin-Chen Chang, Thanos Vasilakos, Yan Zhang, Damien Sauveron, Xingang Wang, Young-Sik Jeong
Pages	219-230
Number of pages	12
DOIs	https://doi.org/10.1007/978-3-642-10238-7_18
Publication status	Published - 2009

Publication series

Name	Communications in Computer and Information Science
Volume	28
ISSN (Print)	1865-0929

Keywords

Disease
HLA
Interaction information
Textmining

ASJC Scopus subject areas

General Computer Science
General Mathematics

Access to Document

10.1007/978-3-642-10238-7_18

Cite this

Chae, J. M., Chae, J. E., Lee, T., Jung, Y., Oh, H., & Jung, S. (2009). Automatic extraction of HLA-disease interaction information from biomedical literature. In T. Kim, L. T. Yang, J. H. Park, A. C.-C. Chang, T. Vasilakos, Y. Zhang, D. Sauveron, X. Wang, & Y.-S. Jeong (Eds.), Advances in Computational Science and Engineering: Second International Conference, FGCN 2008, Workshops and Symposia, Sanya, Hainan Island, China, December 13-15, 2008. Revised Selected Papers (pp. 219-230). (Communications in Computer and Information Science; Vol. 28). https://doi.org/10.1007/978-3-642-10238-7_18

Automatic extraction of HLA-disease interaction information from biomedical literature. / Chae, Jeong Min; Chae, Ji Eun; Lee, Taemin et al.
Advances in Computational Science and Engineering: Second International Conference, FGCN 2008, Workshops and Symposia, Sanya, Hainan Island, China, December 13-15, 2008. Revised Selected Papers. ed. / Tai-hoon Kim; Laurence T. Yang; Jong Hyuk Park; Alan Chin-Chen Chang; Thanos Vasilakos; Yan Zhang; Damien Sauveron; Xingang Wang; Young-Sik Jeong. 2009. p. 219-230 (Communications in Computer and Information Science; Vol. 28).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Chae, JM, Chae, JE, Lee, T, Jung, Y, Oh, H & Jung, S 2009, Automatic extraction of HLA-disease interaction information from biomedical literature. in T Kim, LT Yang, JH Park, AC-C Chang, T Vasilakos, Y Zhang, D Sauveron, X Wang & Y-S Jeong (eds), Advances in Computational Science and Engineering: Second International Conference, FGCN 2008, Workshops and Symposia, Sanya, Hainan Island, China, December 13-15, 2008. Revised Selected Papers. Communications in Computer and Information Science, vol. 28, pp. 219-230. https://doi.org/10.1007/978-3-642-10238-7_18

Chae JM, Chae JE, Lee T, Jung Y, Oh H, Jung S. Automatic extraction of HLA-disease interaction information from biomedical literature. In Kim T, Yang LT, Park JH, Chang ACC, Vasilakos T, Zhang Y, Sauveron D, Wang X, Jeong YS, editors, Advances in Computational Science and Engineering: Second International Conference, FGCN 2008, Workshops and Symposia, Sanya, Hainan Island, China, December 13-15, 2008. Revised Selected Papers. 2009. p. 219-230. (Communications in Computer and Information Science). doi: 10.1007/978-3-642-10238-7_18

Chae, Jeong Min ; Chae, Ji Eun ; Lee, Taemin et al. / Automatic extraction of HLA-disease interaction information from biomedical literature. Advances in Computational Science and Engineering: Second International Conference, FGCN 2008, Workshops and Symposia, Sanya, Hainan Island, China, December 13-15, 2008. Revised Selected Papers. editor / Tai-hoon Kim ; Laurence T. Yang ; Jong Hyuk Park ; Alan Chin-Chen Chang ; Thanos Vasilakos ; Yan Zhang ; Damien Sauveron ; Xingang Wang ; Young-Sik Jeong. 2009. pp. 219-230 (Communications in Computer and Information Science).

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Automatic extraction of HLA-disease interaction information from biomedical literature

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