ci2c01199_si_001.pdf (1.23 MB)
Q‑raKtion: A Semiautomated KNIME Workflow for Bioactivity Data Points Curation
journal contributionposted on 2022-11-28, 22:14 authored by Deborah Palazzotti, Martina Fiorelli, Stefano Sabatini, Serena Massari, Maria Letizia Barreca, Andrea Astolfi
The recent increase of bioactivity data freely available to the scientific community and stored as activity data points in chemogenomic repositories provides a huge amount of ready-to-use information to support the development of predictive models. However, the benefits provided by the availability of such a vast amount of accessible information are strongly counteracted by the lack of uniformity and consistency of data from multiple sources, requiring a process of integration and harmonization. While different automated pipelines for processing and assessing chemical data have emerged in the last years, the curation of bioactivity data points is a less investigated topic, with useful concepts provided but no tangible tools available. In this context, the present work represents a first step toward the filling of this gap, by providing a tool to meet the needs of end-user in building proprietary high-quality data sets for further studies. Specifically, we herein describe Q-raKtion, a systematic, semiautomated, flexible, and, above all, customizable KNIME workflow that effectively aggregates information on biological activities of compounds retrieved by two of the most comprehensive and widely used repositories, PubChem and ChEMBL.
widely used repositoriestangible tools availablepresent work representsless investigated topicherein describe qfirst step towarddifferent automated pipelinescustomizable knime workflowchemogenomic repositories providesbuilding proprietary highquality data setsbioactivity data pointsassessing chemical dataactivity data pointsuseful concepts providedeffectively aggregates informationsemiautomated knime workflowq ‑ raktionbenefits provideduse informationaccessible informationvast amountstrongly counteractedscientific communityrecent increasepredictive modelsmultiple sourceslast yearshuge amountcompounds retrievedbiological activities