Vol. 20 no. 2 2004, pages 216-225
Bioinformatics © Oxford University Press 2004; all rights reserved.
GAPSCORE: finding gene and protein names one word at a time
1 Department of Genetics, Stanford Medical Center, 300 Pasteur Drive, Lane L 301, Mail Code 5120, Stanford, CA 94305-5120, USA and 2 Enkata Technologies, 2121 South El Camino Real, Suite 1200 San Mateo, CA 94403-1855, USA
Received on April 24, 2003
; revised on July 3, 2003
; accepted on July 18, 2003
Motivation: New high-throughput technologies have accelerated the accumulation of knowledge about genes and proteins. However, much knowledge is still stored as written natural language text. Therefore, we have developed a new method, GAPSCORE, to identify gene and protein names in text. GAPSCORE scores words based on a statistical model of gene names that quantifies their appearance, morphology and context.
Results: We evaluated GAPSCORE against the Yapex data set and achieved an F-score of 82.5% (83.3% recall, 81.5% precision) for partial matches and 57.6% (58.5% recall, 56.7% precision) for exact matches. Since the method is statistical, users can choose score cutoffs that adjust the performance according to their needs.
Availability: GAPSCORE is available at http://bionlp.stanford.edu/gapscore/
Contact: russ.altman{at}stanford.edu
* To whom correspondence should be addressed.
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