An Integrative Drug Repurposing Pipeline Using KNIME and Programmatic Data Access: A Case Study on COVID-19 Data
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of flexibility, re-usability, and transparency. Here, we present a strategy for performing in silico drug repurposing with the analytics platform KNIME, using data for 38 suggested COVID-19 drug targets as a timely use case. The workflow includes a targeted download of data through web services, data curation (including chemical structure standardization), detection of enriched structural patterns, as well as substructure searches in DrugBank and a recently deposited dataset of antiviral drugs provided by Chemical Abstracts Service. Developed workflows, tutorials with detailed step-by-step instructions, and the information gained by the analysis of COVID-19 data are made freely available to the scientific community. The provided framework can be reused by researchers for other in silico drug repurposing projects, and it should serve as a valuable teaching resource for conveying integrative data mining strategies.