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PIE: An Online Prediction System for Protein-Protein Interactions from Text



Sun Kim, Soo-Yong Shin, In-Hee Lee, Soo-Jin Kim, Ram D. Sriram, Byoung-Tak Zhang


bio-text mining area, since the PPI information is critical for understanding biological processes. However, there are very few open systems available on the Web and most of the systems focus on keyword searching based on prede¯ned PPIs. PIE (Protein Interaction information Extraction system) is a con¯gurable Web service to extract PPIs from literature, including user-provided papers as well as PubMed articles. After providing abstracts or papers, the prediction results are displayed in an easily readable form with essential, yet compact features. The PIE interface supports more features such as PDF ¯le extraction, PubMed search tool, and network communication, which are useful for biologists and bio-system developers. The PIE system utilizes natural language processing techniques and machine learning methodologies to predict PPI sentences, which results in high precision performance for Web users. PIE is freely available at
Nucleic Acid Research, Special Issue on Web Services


protein-protein interaction sentence prediction, text mining, machine learning, natural language processing, web server


Kim, S. , Shin, S. , Lee, I. , Kim, S. , Sriram, R. and Zhang, B. (2008), PIE: An Online Prediction System for Protein-Protein Interactions from Text, Nucleic Acid Research, Special Issue on Web Services, [online], (Accessed July 21, 2024)


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Created April 16, 2008, Updated October 12, 2021