From Library to Landscape: Integrative Annotation Workflows for Compound Libraries in Drug Repurposing
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This research presents two complementary annotation pipelines (KNIME- and Python-based) that automate the extraction and integration of curated chemical and bioactivity data from public repositories, such as ChEMBL and PubChem. The pipelines were validated on a harmonized subset of the Specs repurposing collection (over 5000 compounds) as part of the REMEDi4ALL project, which aims to establish a European platform for drug repurposing. The researchers also developed interactive dashboards to support multilayered analyses and visualization of chemical properties, bioactivity profiles, and relational data. This framework streamlines data collection and facilitates critical analyses for drug repurposing efforts, while remaining versatile for broader applications in drug discovery. Both pipeline protocols and the dashboards are publicly available, enabling researchers to leverage this powerful tool in their own work.