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


BACKGROUND
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.
http://bionlp.sourceforge.net.
Caporaso
J Gregory
JG
Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO, USA. gregcaporaso@gmail.com
Baumgartner
William A
WA
Randolph
David A
DA
Cohen
K Bretonnel
KB
Hunter
Lawrence
L
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004252:DNA Mutational Analysis; D016206:Databases, Bibliographic; D030541:Databases, Genetic; D030562:Databases, Protein; D005821:Genetic Techniques; D006801:Humans; D009154:Mutation; D010363:Pattern Recognition, Automated; D017354:Point Mutation; D011642:Publications; D015203:Reproducibility of Results; D012984:Software