Towards a Systematic Evaluation of Protein Mutation Extraction Systems

Abstract

The development of text analysis systems targeting the extraction of information about mutations from research publications is an emergent topic in biomedical research. Current systems differ in both scope and approaches, which prevents a meaningful comparison of their performance and therefore possible synergies. To overcome this "evaluation bottleneck," we developed a comprehensive framework for the systematic analysis of mutation extraction systems, precisely defining tasks and corresponding evaluation metrics that will allow a comparison of existing and future applications.

Keywords: mutation extraction systems; mutation evaluation tasks; mutation evaluation metrics

Protein Domains

Reference

René Witte and Christopher J. O. Baker. Towards a Systematic Evaluation of Protein Mutation Extraction Systems. Journal of Bioinformatics and Computational Biology (JBCB), Volume 5, Issue 6, December 2007, pp.1339-1359. PMID: 18172932.

Bibtex entry (also for download):

@Article{WitteBaker07,
  author = 	 {Ren{\'{e}} Witte and Christopher J. O. Baker},
  title = 	 {Towards A Systematic Evaluation of Protein Mutation Extraction Systems},
  journal = 	 {Journal of Bioinformatics and Computational Biology (JBCB)},
  year = 	 {2007},
  volume =	 {5},
  number =	 {6},
  pages =	 {1339--1359},
  month =	 {December},
  pmid =         {18172932},
  note =	 {\url{http://rene-witte.net/evaluation-of-mutation-extraction-systems}}
}

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Copyright © 2007 Imperial College Press. This is the authors' postprint version of the work. It is posted here by permission of World Scientific Publishing for your personal use. Not for redistribution. The definitive version was published in the Journal of Bioinformatics and Computational Biology (JBCB), DOI: 10.1142/S0219720007003193