Abstract
Text mining techniques have been proposed for extracting protein names and their interactions from biological text. 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 also 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 in terms of accuracy and F-measure, requiring significantly less amount of computational time.
This work was supported by grant No. R01-2004-000-10689-0 from the Basic Research Program of the Korea Science & Engineering Foundation.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Ono, T., Hishigaki, H., Tanigami, A., Takagi, T.: Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 17, 155–161 (2001)
Kim, J.D., Ohta, T., Tateisi, Y., Tsujii, J.: Genia corpus - a semantically annotated for bio-textmining. Bioinformatics 19, 180–192 (2002)
Tanabe, L., Wilbur, W.J.: Tagging gene and protein names in full text article. In: Proceedings of Association for Computational Linguistics, pp. 9–13 (2004)
Brill, E.: Some advances in transformation-based part of speech tagging. In: AAAI (1994)
Rinaldi, F., Schneider, G., Kaljurand, K., Dowda’ll, J., Andronis, C., Persidis, A., Konstanti, O.: Mining relations in the genia corpus. In: Proceedings of the Second European Workshop and Text mining for Bioinformatics (2004)
Duda, R.O., Hart, P.E., Stork, D.G.: Pattern Classification, 2nd edn. Wiley-interscience. Inc, Hoboken (2000)
Marcotte, E.M., Xenarios, I., Eisenberg, D.: Mining literature for protein-protein interactions. Bioinformatics 17, 359–363 (2002)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Hong, K., Park, J., Yang, J., Paek, E. (2005). Automatic Extraction of Proteins and Their Interactions from Biological Text. In: Hoffmann, A., Motoda, H., Scheffer, T. (eds) Discovery Science. DS 2005. Lecture Notes in Computer Science(), vol 3735. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11563983_27
Download citation
DOI: https://doi.org/10.1007/11563983_27
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29230-2
Online ISBN: 978-3-540-31698-5
eBook Packages: Computer ScienceComputer Science (R0)