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Briefings in Bioinformatics Advance Access originally published online on October 30, 2007
Briefings in Bioinformatics 2007 8(5):358-375; doi:10.1093/bib/bbm045
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© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Frontiers of biomedical text mining: current progress

Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu and Kevin B. Cohen

Corresponding author. Pierre Zweigenbaum, LIMSI-CNRS, BP 133, 91403 Orsay Cedex, France. Tel: + 33 1 69 85 80 04; Fax: + 33 1 69 85 80 88; E-mail: pz{at}limsi.fr

It is now almost 15 years since the publication of the first paper on text mining in the genomics domain, and decades since the first paper on text mining in the medical domain. Enormous progress has been made in the areas of information retrieval, evaluation methodologies and resource construction. Some problems, such as abbreviation-handling, can essentially be considered solved problems, and others, such as identification of gene mentions in text, seem likely to be solved soon. However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research. In this article we review the current state of the art in biomedical text mining or ‘BioNLP’ in general, focusing primarily on papers published within the past year.

Keywords: text mining, natural language processing, information extraction, text summarization, image mining, question answering, literature-based discovery, evaluation, user orientation

Submitted: May 10, 2007. Received (in revised form): August 15, 2007.


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