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Collective Instance-Level Gene Normalization on the IGN Corpus

Author

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  • Hong-Jie Dai
  • Johnny Chi-Yang Wu
  • Richard Tzong-Han Tsai

Abstract

A high proportion of life science researches are gene-oriented, in which scientists aim to investigate the roles that genes play in biological processes, and their involvement in biological mechanisms. As a result, gene names and their related information turn out to be one of the main objects of interest in biomedical literatures. While the capability of recognizing gene mentions has made significant progress, the results of recognition are still insufficient for direct use due to the ambiguity of gene names. Gene normalization (GN) goes beyond the recognition task by linking a gene mention to a database ID. Unlike most previous works, we approach GN on the instance-level and evaluate its overall performance on the recognition and normalization steps in abstracts and full texts. We release the first instance-level gene normalization (IGN) corpus in the BioC format, which includes annotations for the boundaries of all gene mentions and the corresponding IDs for human gene mentions. Species information, along with existing co-reference chains and full name/abbreviation pairs are also provided for each gene mention. Using the released corpus, we have designed a collective instance-level GN approach using not only the contextual information of each individual instance, but also the relations among instances and the inherent characteristics of full-text sections. Our experimental results show that our collective approach can achieve an F-score of 0.743. The proposed approach that exploits section characteristics in full-text articles can improve the F-scores of information lacking sections by up to 1.8%. In addition, using the proposed refinement process improved the F-score of gene mention recognition by 0.125 and that of GN by 0.03. Whereas current experimental results are limited to the human species, we seek to continue updating the annotations of the IGN corpus and observe how the proposed approach can be extended to other species.

Suggested Citation

  • Hong-Jie Dai & Johnny Chi-Yang Wu & Richard Tzong-Han Tsai, 2013. "Collective Instance-Level Gene Normalization on the IGN Corpus," PLOS ONE, Public Library of Science, vol. 8(11), pages 1-10, November.
    • Handle: RePEc:plo:pone00:0079517
    DOI: 10.1371/journal.pone.0079517
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    References listed on IDEAS

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    1. Doug Howe & Maria Costanzo & Petra Fey & Takashi Gojobori & Linda Hannick & Winston Hide & David P. Hill & Renate Kania & Mary Schaeffer & Susan St Pierre & Simon Twigger & Owen White & Seung Yon Rhee, 2008. "The future of biocuration," Nature, Nature, vol. 455(7209), pages 47-50, September.
    2. Sofie Van Landeghem & Jari Björne & Chih-Hsuan Wei & Kai Hakala & Sampo Pyysalo & Sophia Ananiadou & Hung-Yu Kao & Zhiyong Lu & Tapio Salakoski & Yves Van de Peer & Filip Ginter, 2013. "Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-12, April.
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