Automated extraction of information on protein-protein interactions from the biological literature.
BACKGROUND
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.


BACKGROUND
The program is available on request from the authors.
Ono
T
T
Otsuka GEN Research Institute, Otsuka Pharmaceutical Co. Ltd, 463-10 Kagasuno, Kawauchi-cho, Tokushima, 771-0192, Japan. ono@otsuka.gr.jp
Hishigaki
H
H
Tanigami
A
A
Takagi
T
T
D001330:Electronic Data Processing; D016247:Information Storage and Retrieval; D008091:Literature; D011506:Proteins / Q000378:metabolism*
D011506:Proteins