Mining patterns of drug-disease association from biomedical texts

Wen Juan Hou, Bo Syun Lee, Hung Chi Chen

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

Abstract

Drug repurposing aims to identify new indications for approved drugs, and it can promisingly reduce time and drug development costs. The goal of the paper, drug-disease relation extraction automatically from biomedical texts, is fundamental to the study of drug repurposing since lots of clinical case studies published in an unstructured textual form. To analyze the number of verbs and nouns pertinent to diseases and medications in the training data, two models with different drug-disease orders are established, and some rules are proposed at this phase. The first model is for the sentences with the order that the disease name precedes the drug name. The second model is for the reverse order to the first model. These verbs and nouns are then classified into categories of "pure association," "pure no association" and "neutrals." Among them, some neutrals are further verified by the Chi-square test method. As a result, the associations between diseases and medications are identified, which are called patterns later. Finally, the patterns are used in the test data to extract the disease and drug pairs. The best experimental results show the precision value of 100%, recall value of 89.0%, and F-score value of 94.2%.

Original languageEnglish
Title of host publicationProceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018
PublisherAssociation for Computing Machinery
Pages84-90
Number of pages7
ISBN (Electronic)9781450353410
DOIs
Publication statusPublished - 2018 Jan 18
Event8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018 - Tokyo, Japan
Duration: 2018 Jan 182018 Jan 20

Publication series

NameACM International Conference Proceeding Series

Other

Other8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018
CountryJapan
CityTokyo
Period18/1/1818/1/20

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Keywords

  • Biomedical literature
  • Chi-square test
  • Drug-disease association
  • Pattern extraction

ASJC Scopus subject areas

  • Software
  • Human-Computer Interaction
  • Computer Vision and Pattern Recognition
  • Computer Networks and Communications

Cite this

Hou, W. J., Lee, B. S., & Chen, H. C. (2018). Mining patterns of drug-disease association from biomedical texts. In Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018 (pp. 84-90). (ACM International Conference Proceeding Series). Association for Computing Machinery. https://doi.org/10.1145/3180382.3180401

Mining patterns of drug-disease association from biomedical texts. / Hou, Wen Juan; Lee, Bo Syun; Chen, Hung Chi.

Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018. Association for Computing Machinery, 2018. p. 84-90 (ACM International Conference Proceeding Series).

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

Hou, WJ, Lee, BS & Chen, HC 2018, Mining patterns of drug-disease association from biomedical texts. in Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018. ACM International Conference Proceeding Series, Association for Computing Machinery, pp. 84-90, 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018, Tokyo, Japan, 18/1/18. https://doi.org/10.1145/3180382.3180401
Hou WJ, Lee BS, Chen HC. Mining patterns of drug-disease association from biomedical texts. In Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018. Association for Computing Machinery. 2018. p. 84-90. (ACM International Conference Proceeding Series). https://doi.org/10.1145/3180382.3180401
Hou, Wen Juan ; Lee, Bo Syun ; Chen, Hung Chi. / Mining patterns of drug-disease association from biomedical texts. Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018. Association for Computing Machinery, 2018. pp. 84-90 (ACM International Conference Proceeding Series).
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