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Asia Information Retrieval Symposium

AIRS 2005: Information Retrieval Technology pp 552–557Cite as

Gene Ontology Classification of Biomedical Literatures Using Context Association

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Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 3689))

Abstract

The functional annotation of gene products from biomedical literatures has become a pressing issue due to the huge human efforts involved and the evolving biomedical knowledge. In this paper, we propose an approach for facilitating this functional annotation to the Gene Ontology by focusing on a subtask of annotation, that is, to determine which of the Gene Ontology a literature is associated with. This subtask can be formulated as a document classification problem. A feature engineering approach using context association conveyed in the biomedical literatures, in particular, utilizing the proximity relationship between target gene(s) and term features is proposed. Our approach achieves an F-score of 60.24%, which outperforms the submission runs of TREC Genomics 2004 annotation hierarchy subtask. We show that incorporation of context association can enhance the performance of the annotation hierarchy classification problem.

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Author information

Authors and Affiliations

  1. Department of Systems Engineering and Engineering Management, The Chinese University of Hong Kong, Shatin, Hong Kong

    Ki Chan & Wai Lam

Authors
  1. Ki Chan
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  2. Wai Lam
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Editor information

Editors and Affiliations

  1. Department of Computer Science and Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Nam-gu, 790-784, Pohang, Korea

    Gary Geunbae Lee

  2. Computer and Communication Media Research, NEC Corp., Miyazaki 4-1-1, Miyamae-ku, 216-8555, Kawasaki, Japan

    Akio Yamada

  3. Human-Computer Communications Laboratory, Department of Systems Engineering and Engineering Management, The Chinese University of Hong Kong, Hong Kong

    Helen Meng

  4. School of Engineering, Information and Communications University, 119, Munjiro, Yuseong-gu, 305-732, Daejeon, Korea

    Sung Hyon Myaeng

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© 2005 Springer-Verlag Berlin Heidelberg

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Chan, K., Lam, W. (2005). Gene Ontology Classification of Biomedical Literatures Using Context Association. In: Lee, G.G., Yamada, A., Meng, H., Myaeng, S.H. (eds) Information Retrieval Technology. AIRS 2005. Lecture Notes in Computer Science, vol 3689. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11562382_49

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  • DOI: https://doi.org/10.1007/11562382_49

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-29186-2

  • Online ISBN: 978-3-540-32001-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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