Extracting interactions between proteins from the literature

Deyu Zhou, Yulan He

Research output: Contribution to journalArticlepeer-review


During the last decade, biomedicine has witnessed a tremendous development. Large amounts of experimental and computational biomedical data have been generated along with new discoveries, which are accompanied by an exponential increase in the number of biomedical publications describing these discoveries. In the meantime, there has been a great interest with scientific communities in text mining tools to find knowledge such as protein-protein interactions, which is most relevant and useful for specific analysis tasks. This paper provides a outline of the various information extraction methods in biomedical domain, especially for discovery of protein-protein interactions. It surveys methodologies involved in plain texts analyzing and processing, categorizes current work in biomedical information extraction, and provides examples of these methods. Challenges in the field are also presented and possible solutions are discussed.
Original languageEnglish
Pages (from-to)393-407
Number of pages15
JournalJournal of Biomedical Informatics
Issue number2
Publication statusPublished - Apr 2008

Bibliographical note

NOTICE: this is the author’s version of a work that was accepted for publication in Journal of biomedical informatics. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Zhou, D & He, Y 2008, 'Extracting interactions between proteins from the literature' Journal of biomedical informatics, vol. 41, no. 2 (2008) DOI http://dx.doi.org/10.1016/j.jbi.2007.11.008.


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