Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion

Jitendra Jonnagaddala, Toni Rose Jue, Nai-Wen Chang, Hong-Jie Dai
2016 Database: The Journal of Biological Databases and Curation  
Citation details: Jonnagaddala,J., Jue,T.R., Chang,N.-W. and Dai,H.-J. Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion. Abstract The rapidly increasing biomedical literature calls for the need of an automatic approach in the recognition and normalization of disease mentions in order to increase the precision and effectivity of disease based information retrieval. A variety of methods have been proposed to deal with the problem of
more » ... isease named entity recognition and normalization. Among all the proposed methods, conditional random fields (CRFs) and dictionary lookup method are widely used for named entity recognition and normalization respectively. We herein developed a CRF-based model to allow automated recognition of disease mentions, and studied the effect of various techniques in improving the normalization results based on the dictionary lookup approach. The dataset from the BioCreative V CDR track was used to report the performance of the developed normalization methods and compare with other existing dictionary lookup based normalization methods. The best configuration achieved an F-measure of 0.77 for the disease normalization, which outperformed the best dictionary lookup based baseline method studied in this work by an F-measure of 0.13.
doi:10.1093/database/baw112 pmid:27504009 pmcid:PMC4976299 fatcat:bproo6ouo5hjlgmukudmhvo6ay