BiOmics Case Study.

This dataset contains the input data, analysis scripts, intermediate artifacts, execution logs, and final figures used to reproduce the computational case studies presented in the BiOmics manuscript. Covered tasks include cell-type annotation and subtype refinement,differential-expression and enrichment analysis, cellular trajectory inference, GWAS variant interpretation and phenotype assignment, proteomics and protein–protein interaction analysis, gene-regulatory-network analysis, and drug repurposing. The archive is organized by task and includes original input data or dataset accession information, BiOmics-KG query results, analysis and visualization scripts, intermediate files, final publication-ready figures, run summaries, and agent execution logs where available. These materials document how BiOmics-BRICK and agent-orchestrated workflows were applied to each analysis and are intended to support transparent evaluation, independent reuse, and reproducibility of the reported results. Any methodological deviations, fallback procedures, and KG-version-dependent differences are documented in the corresponding run summaries.