Event extraction for gene regulation network using syntactic and semantic approaches

Wen Juan Hou, Bamfa Ceesay

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

3 Citations (Scopus)

Abstract

Gene Regulation Network (GRN) is a graphical representation of the relationship between molecular mechanisms and cellular behavior in system biology. This paper examines the extraction of GRN from biological literatures using text mining techniques. The study proposes two independent methods first, a syntactic method and a semantic method in text mining, to extract biological events from the unstructured text. The paper presents the performance of the two methods and then experiments with the combined strategy to construct a gene regulation network from texts. The results show that the graph-based approach obtains a better result on event extraction and produces a much better regulation network than the semantic analysis method. The combination of the two approaches has yet a much slightly better result than that with the individual approach. This exhilarates us to find more future directions in the biological event extraction research.

Original languageEnglish
Title of host publicationCurrent Approaches in Applied Artificial Intelligence - 28th International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2015, Proceedings
EditorsChang-Hwan Lee, Yongdai Kim, Young Sig Kwon, Juntae Kim, Moonis Ali
PublisherSpringer Verlag
Pages559-570
Number of pages12
ISBN (Print)9783319190655
DOIs
Publication statusPublished - 2015 Jan 1
Event28th International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2015 - Seoul, Korea, Republic of
Duration: 2015 Jun 102015 Jun 12

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9101
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other28th International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2015
CountryKorea, Republic of
CitySeoul
Period15/6/1015/6/12

Fingerprint

Gene Regulation
Syntactics
Gene expression
Semantics
Text Mining
Semantic Analysis
Graphical Representation
Systems Biology
Syntax
Experiments
Graph in graph theory
Experiment

Keywords

  • Biological event extraction
  • Gene regulation network
  • Graph-based approach
  • Semantic approach
  • Slot error rate

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Hou, W. J., & Ceesay, B. (2015). Event extraction for gene regulation network using syntactic and semantic approaches. In C-H. Lee, Y. Kim, Y. S. Kwon, J. Kim, & M. Ali (Eds.), Current Approaches in Applied Artificial Intelligence - 28th International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2015, Proceedings (pp. 559-570). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9101). Springer Verlag. https://doi.org/10.1007/978-3-319-19066-2_54

Event extraction for gene regulation network using syntactic and semantic approaches. / Hou, Wen Juan; Ceesay, Bamfa.

Current Approaches in Applied Artificial Intelligence - 28th International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2015, Proceedings. ed. / Chang-Hwan Lee; Yongdai Kim; Young Sig Kwon; Juntae Kim; Moonis Ali. Springer Verlag, 2015. p. 559-570 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9101).

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

Hou, WJ & Ceesay, B 2015, Event extraction for gene regulation network using syntactic and semantic approaches. in C-H Lee, Y Kim, YS Kwon, J Kim & M Ali (eds), Current Approaches in Applied Artificial Intelligence - 28th International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2015, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9101, Springer Verlag, pp. 559-570, 28th International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2015, Seoul, Korea, Republic of, 15/6/10. https://doi.org/10.1007/978-3-319-19066-2_54
Hou WJ, Ceesay B. Event extraction for gene regulation network using syntactic and semantic approaches. In Lee C-H, Kim Y, Kwon YS, Kim J, Ali M, editors, Current Approaches in Applied Artificial Intelligence - 28th International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2015, Proceedings. Springer Verlag. 2015. p. 559-570. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-319-19066-2_54
Hou, Wen Juan ; Ceesay, Bamfa. / Event extraction for gene regulation network using syntactic and semantic approaches. Current Approaches in Applied Artificial Intelligence - 28th International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2015, Proceedings. editor / Chang-Hwan Lee ; Yongdai Kim ; Young Sig Kwon ; Juntae Kim ; Moonis Ali. Springer Verlag, 2015. pp. 559-570 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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