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Bioinformatics. 2007 Jul 15;23(14):1862-5. Epub 2007 May 11.

MutationFinder: a high-performance system for extracting point mutation mentions from text.

Author information

1
Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO, USA. gregcaporaso@gmail.com

Abstract

Discussion of point mutations is ubiquitous in biomedical literature, and manually compiling databases or literature on mutations in specific genes or proteins is tedious. We present an open-source, rule-based system, MutationFinder, for extracting point mutation mentions from text. On blind test data, it achieves nearly perfect precision and a markedly improved recall over a baseline.

AVAILABILITY:

MutationFinder, along with a high-quality gold standard data set, and a scoring script for mutation extraction systems have been made publicly available. Implementations, source code and unit tests are available in Python, Perl and Java. MutationFinder can be used as a stand-alone script, or imported by other applications.

PROJECT URL:

http://bionlp.sourceforge.net.

PMID:
17495998
PMCID:
PMC2516306
DOI:
10.1093/bioinformatics/btm235
[Indexed for MEDLINE]
Free PMC Article

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