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Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature.
Lee, Kyubum; Wei, Chih-Hsuan; Lu, Zhiyong.
Afiliação
  • Lee K; National Center for Biotechnology Information.
  • Wei CH; National Center for Biotechnology Information.
  • Lu Z; National Center for Biotechnology Information.
Brief Bioinform ; 22(3)2021 05 20.
Article em En | MEDLINE | ID: mdl-32770181
MOTIVATION: To obtain key information for personalized medicine and cancer research, clinicians and researchers in the biomedical field are in great need of searching genomic variant information from the biomedical literature now than ever before. Due to the various written forms of genomic variants, however, it is difficult to locate the right information from the literature when using a general literature search system. To address the difficulty of locating genomic variant information from the literature, researchers have suggested various solutions based on automated literature-mining techniques. There is, however, no study for summarizing and comparing existing tools for genomic variant literature mining in terms of how to search easily for information in the literature on genomic variants. RESULTS: In this article, we systematically compared currently available genomic variant recognition and normalization tools as well as the literature search engines that adopted these literature-mining techniques. First, we explain the problems that are caused by the use of non-standard formats of genomic variants in the PubMed literature by considering examples from the literature and show the prevalence of the problem. Second, we review literature-mining tools that address the problem by recognizing and normalizing the various forms of genomic variants in the literature and systematically compare them. Third, we present and compare existing literature search engines that are designed for a genomic variant search by using the literature-mining techniques. We expect this work to be helpful for researchers who seek information about genomic variants from the literature, developers who integrate genomic variant information from the literature and beyond.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Variação Genética / Medicina de Precisão / Mineração de Dados / Ferramenta de Busca Tipo de estudo: Risk_factors_studies Idioma: En Ano de publicação: 2021 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Variação Genética / Medicina de Precisão / Mineração de Dados / Ferramenta de Busca Tipo de estudo: Risk_factors_studies Idioma: En Ano de publicação: 2021 Tipo de documento: Article