Bioinformatics Vol. 17 no. 2 2001
Pages 155-161
© 2001 Oxford University Press
Original Paper |
Automated extraction of information on protein–protein interactions from the biological literature
1 Otsuka GEN Research Institute, Otsuka
Pharmaceutical Co. Ltd, 463-10 Kagasuno, Kawauchi-cho, Tokushima,
771-0192, Japan
2 Human Genome Center, Institute of Medical
Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku,
Tokyo, 108-8639, Japan
Received on September 11, 2000
; revised on September 13, 2000
; accepted on September 28, 2000
Motivation: To understand biological process, we must clarify how proteins interact with each other. However, since information about protein–protein interactions still exists primarily in the scientific literature, it is not accessible in a computer-readable format. Efficient processing of large amounts of interactions therefore needs an intelligent information extraction method. Our aim is to develop an efficient method for extracting information on protein–protein interaction from scientific literature.
Results: We present a method for extracting information on
protein–protein interactions from the scientific literature.
This method, which employs only a protein name dictionary, surface
clues on word patterns and simple part-of-speech rules, achieved
high recall and precision rates for yeast (recall 
86.8% and
precision 94.3%) and Escherichia coli (recall 82.5%
and precision 93.5%). The result of extraction suggests that
our method should be applicable to any species for which a protein
name dictionary is constructed.
Availability: The program is available on request from the authors.
Contact: ono{at}otsuka.gr.jp
* To whom correspondence should be addressed.
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