BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm056 Data and text mining Gene symbol disambiguation using knowledge-based profiles

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BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm056 Data and text mining Gene symbol disambiguation using knowledge-based profiles

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by Hua Xu , Jung-wei Fan , George Hripcsak , Eneida A. Mendonça , Marianthi Markatou , Carol Friedman

BibTeX

@MISC{Xu_bioinformaticsoriginal,
    author = {Hua Xu and Jung-wei Fan and George Hripcsak and Eneida A. Mendonça and Marianthi Markatou and Carol Friedman},
    title = {BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm056 Data and text mining Gene symbol disambiguation using knowledge-based profiles},
    year = {}
}

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Abstract

Motivation: The ambiguity of biomedical entities, particularly of gene symbols, is a big challenge for text-mining systems in the biomedical domain. Existing knowledge sources, such as Entrez Gene and the MEDLINE database, contain information concerning the characteristics of a particular gene that could be used to disambiguate gene symbols. Results: For each gene, we create a profile with different types of information automatically extracted from related MEDLINE abstracts and readily available annotated knowledge sources. We apply the gene profiles to the disambiguation task via an information retrieval method, which ranks the similarity scores between the context where the ambiguous gene is mentioned, and candidate gene profiles. The gene profile with the highest similarity score is then chosen as the correct sense. We evaluated the method on three automatically generated testing sets of mouse, fly and yeast organisms, respectively. The method achieved the highest precision of 93.9 % for the mouse, 77.8 % for the fly and 89.5 % for the yeast. Availability: The testing data sets and disambiguation programs are available at

Keyphrases

text mining gene symbol disambiguation gene profile bioinformatics original paper doi knowledge-based profile bioinformatics btm056 data gene symbol knowledge source medline database related medline abstract biomedical domain disambiguation task yeast organism biomedical entity disambiguation program contain information big challenge entrez gene correct sense similarity score different type data set information retrieval method ambiguous gene text-mining system particular gene

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