SilkRoute Case Studies: Workflow Configurations, Biomolecular Datasets, and Provenance Metadata

This repository contains the workflow configurations, generated datasets, and provenance records associated with three SilkRoute case studies covering protein, compound, and interaction data acquisition. The deposited workflows include: (i) the retrieval and enrichment of reviewed antimicrobial proteins using UniProt, AlphaFold DB, InterPro, PDB, and Pathway Commons; (ii) the acquisition and composition of ChEMBL compound bioactivity records based on IC50 measurements; and (iii) the construction of an interaction-aware protein dataset using protein and molecular interaction resources. The deposit includes the YAML configuration file for each workflow, the complete tabular outputs, exported graph data where applicable, and machine-readable provenance and execution records. These materials support the reproduction, inspection, and reuse of the SilkRoute case studies presented in the associated article. The workflows were executed using SilkRoute version 0.1.0. For detailed instructions, file descriptions, and workflow execution commands, see the included README.md