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        Text Mining of Biomedical Articles Using the Konstanz Information Miner (KNIME) Platform: Hemolytic Uremic Syndrome as a Case Study

        Ricardo A. Dorr,Juan J. Casal,Roxana Toriano 대한의료정보학회 2022 Healthcare Informatics Research Vol.28 No.3

        Objectives: Automated systems for information extraction are becoming very useful due to the enormous scale of the existingliterature and the increasing number of scientific articles published worldwide in the field of medicine. We aimed todevelop an accessible method using the open-source platform KNIME to perform text mining (TM) on indexed publications. Material from scientific publications in the field of life sciences was obtained and integrated by mining information onhemolytic uremic syndrome (HUS) as a case study. Methods: Text retrieved from Europe PubMed Central (PMC) was processedusing specific KNIME nodes. The results were presented in the form of tables or graphical representations. Data couldalso be compared with those from other sources. Results: By applying TM to the scientific literature on HUS as a case study,and by selecting various fields from scientific articles, it was possible to obtain a list of individual authors of publications,build bags of words and study their frequency and temporal use, discriminate topics (HUS vs. atypical HUS) in an unsupervisedmanner, and cross-reference information with a list of FDA-approved drugs. Conclusions: Following the instructionsin the tutorial, researchers without programming skills can successfully perform TM on the indexed scientific literature. Thismethodology, using KNIME, could become a useful tool for performing statistics, analyzing behaviors, following trends, andmaking forecast related to medical issues. The advantages of TM using KNIME include enabling the integration of scientificinformation, helping to carry out reviews, and optimizing the management of resources dedicated to basic and clinical research.

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