An Evidence Qualification Framework for Annotation-Level Formula Discrimination in Traditional Chinese Medicine: PLOS ONE submission package

This reproducibility compendium supports an evidence-gated computational study of Shen-Qi-Run-Chang Decoction (SQRCD) for constipation. Sixteen herbs were reconstructed without oral-bioavailability or drug-likeness exclusion, while chemical identity and provenance uncertainty were retained. The workflow separates database-reconstructed constituents, experimental and predicted compound–target relations, constipation-related disease evidence, human genetics, non-neoplastic intestinal transcriptomics, perturbational connectivity, pre-specified formula ablation and structural quality control. The reconstruction comprised 7,038 herb–constituent source records and 2,657 provisional compounds, including 1,603 compounds with resolved structures. Evidence gating reduced the discovery space to 257 experimental compound–gene pairs and 42 disease-supported pairs. No tested genetic family produced a multiplicity-controlled and colocalized candidate. Repeated-measures analysis of GSE36701 identified a modest human IBS-C colon-mucosal signature and ranked evidence for altered translational and bioenergetic programs, but no SQRCD constituent mapped with high confidence to the leading exploratory L1000 reversing perturbations. All 19 pre-specified formula variants therefore lacked an estimable formula-specific reversal endpoint, and the stopping rule was applied before production molecular dynamics. The archive contains analysis scripts, processed statistical outputs, publication-quality figures, the full manuscript, a data dictionary, source-accession information and SHA-256 checksums. Raw GEO files and third-party database exports are not redistributed. The results support computational reproducibility and evidence auditing; they do not demonstrate clinical efficacy or experimentally validated formula optimization.