Inter-sentence relation extraction for associating biological context with events in biomedical texts

Enrique Noriega-Atala, Paul Douglas Hein, Shraddha Satish Thumsi, Zechy Wong, Xia Wang, Clayton T Morrison

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

2 Scopus citations

Abstract

We present an analysis of the problem of identifying biological context and associating it with biochemical events in biomedical texts. This constitutes a non-trivial, inter-sentential relation extraction task. We focus on biological context as descriptions of the species, tissue type and cell type that are associated with biochemical events. We describe the properties of an annotated corpus of context-event relations and present and evaluate several classifiers for context-event association trained on syntactic, distance and frequency features.

Original languageEnglish (US)
Title of host publicationProceedings - 18th IEEE International Conference on Data Mining Workshops, ICDMW 2018
EditorsJeffrey Yu, Zhenhui Li, Hanghang Tong, Feida Zhu
PublisherIEEE Computer Society
Pages722-731
Number of pages10
ISBN (Electronic)9781538692882
DOIs
StatePublished - Feb 7 2019
Event18th IEEE International Conference on Data Mining Workshops, ICDMW 2018 - Singapore, Singapore
Duration: Nov 17 2018Nov 20 2018

Publication series

NameIEEE International Conference on Data Mining Workshops, ICDMW
Volume2018-November
ISSN (Print)2375-9232
ISSN (Electronic)2375-9259

Conference

Conference18th IEEE International Conference on Data Mining Workshops, ICDMW 2018
CountrySingapore
CitySingapore
Period11/17/1811/20/18

Keywords

  • bioinformatics
  • context
  • data mining
  • NLP
  • relation-extraction

ASJC Scopus subject areas

  • Computer Science Applications
  • Software

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  • Cite this

    Noriega-Atala, E., Hein, P. D., Thumsi, S. S., Wong, Z., Wang, X., & Morrison, C. T. (2019). Inter-sentence relation extraction for associating biological context with events in biomedical texts. In J. Yu, Z. Li, H. Tong, & F. Zhu (Eds.), Proceedings - 18th IEEE International Conference on Data Mining Workshops, ICDMW 2018 (pp. 722-731). [8637510] (IEEE International Conference on Data Mining Workshops, ICDMW; Vol. 2018-November). IEEE Computer Society. https://doi.org/10.1109/ICDMW.2018.00110