Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

This article is part of the supplement: The BioCreative II - Critical Assessment for Information Extraction in Biology Challenge

Open Access Open Badges Research

Mining physical protein-protein interactions from the literature

Minlie Huang, Shilin Ding, Hongning Wang and Xiaoyan Zhu*

Author affiliations

State Key Laboratory of Intelligent Technology and Systems, Tsinghua National Laboratory for Information Science and Technology, Department of Computer Science and Technology, Tsinghua Park No. 1, Tsinghua University, Beijing 100084, China

For all author emails, please log on.

Citation and License

Genome Biology 2008, 9(Suppl 2):S12  doi:10.1186/gb-2008-9-s2-s12

Published: 1 September 2008



Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual curation is intensive in terms of time and cost, there is an urgent need for text-mining tools to facilitate the extraction of such information. The BioCreative (Critical Assessment of Information Extraction systems in Biology) challenge evaluation provided common standards and shared evaluation criteria to enable comparisons among different approaches.


During the benchmark evaluation of BioCreative 2006, all of our results ranked in the top three places. In the task of filtering articles irrelevant to physical protein interactions, our method contributes a precision of 75.07%, a recall of 81.07%, and an AUC (area under the receiver operating characteristic curve) of 0.847. In the task of identifying protein mentions and normalizing mentions to molecule identifiers, our method is competitive among runs submitted, with a precision of 34.83%, a recall of 24.10%, and an F1 score of28.5%. In extracting protein interaction pairs, our profile-based method was competitive on the SwissProt-only subset (precision = 36.95%, recall = 32.68%, and F1 score = 30.40%) and on the entire dataset (30.96%, 29.35%, and26.20%, respectively). From the biologist's point of view, however, these findings are far from satisfactory. The error analysis presented in this report provides insight into how performance could be improved: three-quarters of false negatives were due to protein normalization problems (532/698), and about one-quarter were due to problems with correctly extracting interactions for this system.


We present a text-mining framework to extract physical protein-protein interactions from the literature. Three key issues are addressed, namely filtering irrelevant articles, identifying protein names and normalizing them to molecule identifiers, and extracting protein-protein interactions. Our system is among the top three performers in the benchmark evaluation of BioCreative 2006. The tool will be helpful for manual interaction curation and can greatly facilitate the process of extracting protein-protein interactions.