Biological Text Mining for Extraction of Proteins and Their Interactions

  • Kiho Hong
  • Junhyung Park
  • Jihoon Yang
  • Sungyong Park
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3776)


Text mining techniques have been proposed for extracting protein names and their interactions. First, we have made improvements on existing methods for handling single word protein names consisting of characters, special symbols, and numbers. Second, compound word protein names are extracted using conditional probabilities of the occurrences of neighboring words. Third, interactions are extracted based on Bayes theorem over discriminating verbs that represent the interactions of proteins. Experimental results demonstrate the feasibility of our approach with improved performance.


  1. 1.
    Ono, T.: Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 17, 155–161 (2001)CrossRefGoogle Scholar
  2. 2.
    Brill, E.: Some advances in transformation-based part of speech tagging. In: AAAI (1994)Google Scholar
  3. 3.
    Kim, J.D., Ohta, T., Tateisi, Y., Tsujii, J.: Genia corpus - a semantically annotated for bio-textmining. Bioinformatics 19, 180–192 (2002)CrossRefGoogle Scholar
  4. 4.
    Rinaldi, F.: Mining relations in the genia corpus. In: Proceedings of the Second European Workshop and Text mining for Bioinformatics (2004)Google Scholar
  5. 5.
    Tanabe, L., Wilbur, W.J.: Tagging gene and protein names in full text article. In: Proceedings of Association for Computational Linguistics, 9–13 (2004)Google Scholar
  6. 6.
    Duda, R.O.: Pattern Classification, 2nd edn., pp. 128–138. Wiley-interscience. Inc., Hoboken (2000)Google Scholar
  7. 7.
    Marcotte, E. M.: Mining literature for protein-protein interactions. Bioinformatics 17, 359–363 (2002)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Kiho Hong
    • 1
  • Junhyung Park
    • 2
  • Jihoon Yang
    • 2
  • Sungyong Park
    • 2
  1. 1.IT Agent Research Lab, LSIS R&D CenterKyungki-DoKorea
  2. 2.Department of Computer Science and Interdisciplinary Program of Integrated BiotechnologySogang UniversitySeoulKorea

Personalised recommendations