title: 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 disease 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.Database URL: https://github.com/TCRNBioinformatics/DiseaseExtract.
authors: School of Public Health and Community Medicine, UNSW, Kensington, NSW 2033, Australia Prince of Wales Clinical School, UNSW, Kensington, NSW 2033, Australia z33339253@unsw.edu.au hjdai@nttu.edu.tw.
authors: Jitendra
authors: J
authors: Jonnagaddala
authors: Prince of Wales Clinical School, UNSW, Kensington, NSW 2033, Australia.
authors: Toni Rose
authors: TR
authors: Jue
authors: Institution of Information Science, Academia Sinica, Taipei 115, Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan and.
authors: Nai-Wen
authors: NW
authors: Chang
authors: Department of Computer Science and Information Engineering, National Taitung University, Taipei, Taiwan z33339253@unsw.edu.au hjdai@nttu.edu.tw.
authors: Hong-Jie
authors: HJ
authors: Dai
mesh_terms: D057225:Data Mining / Q000379:methods*; D004018:Dictionaries, Medical as Topic; D001330:Electronic Data Processing / Q000379:methods*; D006801:Humans