Automatic extraction of proteins and their interactions from biological text

Authors:
Kiho Hong;Junhyung Park;Jihoon Yang;Eunok Paek
Affiliations:
IT Agent Research Lab, LSIS R&D Center, Kyungki-Do, Korea;Department of Computer Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Korea;Department of Computer Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Korea;Department of Mechanical and Information Engineering, The University of Seoul, Seoul, Korea
Venue:
DS'05 Proceedings of the 8th international conference on Discovery Science
Year:
2005

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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.