Conference Paper

The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature

  1. Satoko Yamamoto1,
  2. Takao Asanuma1,
  3. Toshihisa Takagi2,
  4. Ken Ichiro Fukuda3,*

Article first published online: 6 JAN 2005

DOI: 10.1002/cfg.432

Issue

Comparative and Functional Genomics

Comparative and Functional Genomics

Volume 5, Issue 6-7, pages 528–536, August - October 2004

Additional Information

How to Cite

Yamamoto, S., Asanuma, T., Takagi, T. and Fukuda, K. I. (2004), The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature. Comparative and Functional Genomics, 5: 528–536. doi: 10.1002/cfg.432

Author Information

  1. 1

    Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Tokyo, Japan

  2. 2

    Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan

  3. 3

    Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan

*Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2–43 Aomi, Koutou-ku, Tokyo 135-0064, Japan.

Publication History

  1. Issue published online: 6 JAN 2005
  2. Article first published online: 6 JAN 2005
  3. Manuscript Accepted: 22 OCT 2004
  4. Manuscript Revised: 20 OCT 2004
  5. Manuscript Received: 5 OCT 2004

Funded by

  • Science and Technology Agency, Japan
  • Ministry of Education, Culture, Sports, Science and Technology, Japan

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Keywords:

  • ontology;
  • signal transduction;
  • text mining;
  • scientific literature;
  • pathway database;
  • annotation;
  • manual curation;
  • molecule name;
  • protein name dictionary

Abstract

In general, it is not easy to specify a single sequence identity for each molecule name that appears in a pathway in the scientific literature. A molecule name may stand for concepts of various granularities, from concrete objects such as H-Ras and ERK1 to abstract concepts or categories such as Ras and MAPK. Typically, the relations among molecule names derive a hierarchical structure; without a proper way to handle this knowledge, it becomes ever more difficult to develop a reliable pathway database. This paper describes an ontology that is designed to annotate molecules in the scientific literature on signal transduction pathways. Copyright © 2004 John Wiley & Sons, Ltd.

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