alexa MutationFinder: a high-performance system for extracting point mutation mentions from text.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Health & Medical Informatics

Author(s): Caporaso JG, Baumgartner WA Jr, Randolph DA, Cohen KB, Hunter L

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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.
This article was published in Bioinformatics and referenced in Journal of Health & Medical Informatics

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