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A GAPSCORE System is a Protein NER System.



  • (Chang et al., 2004) ⇒ Jeffrey T. Chang, Hinrich Schütze, and Russ B. Altman. (2004). “GAPSCORE: finding gene and protein names one word at a time.” In: Bioinformatics, 20(2).
    • 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