Reproducibility Package for Evaluating ChEMBL's Potential-Duplicate Annotation in Molecular Benchmarks

Version 1.0.1 corrects a document-type label and reproducibility coverage. The 1,056-pair residual stratum was incorrectly described as DATASET-involving; it contains 756 PATENT-PUBLICATION pairs and 300 pairs involving a DATASET document. The underlying counts and all CARA/NTAB confirmatory values are unchanged. Version 1.0.0's description incorrectly stated that the unaudited historical ml_impact files were excluded; they were present, and version 1.0.1 removes them. This version also adds deterministic post-hoc reference scripts for the rounding simulation and the tier-2 cross-target organism comparison, and discloses that the source text of the hashed 20-pair citation-check protocol and the tier-1 activity snapshot were not recovered. Reproducibility package supporting the manuscript “Evaluating ChEMBL's Potential-Duplicate Annotation in Molecular Benchmarks”. The archive contains ChEMBL 37-derived activity and pair-level data, the complete potential_duplicate snapshot, frozen preregistrations and amendments, blinded audit materials and de-identified coding, citation-check outputs, and the CARA LO-GPCR and NTAB confirmatory protocols, authorized scripts, outputs, and integrity manifests. Two historical code-provenance gaps are explicitly documented. The initially archived pair-builder variant omitted activity-ID fields required downstream; the original, a minimal reconstruction, and a portable reference version are retained. The three-level bootstrap table came from an unarchived interactive calculation on 2026-07-29; bootstrap_ci.py is a post-hoc reference reimplementation written on 2026-07-30 that reproduces all reported intervals but is not represented as the original code. Version 1.0.1 excludes the unaudited historical ml_impact analysis and contains no RRE or FTO materials. Public source datasets retain their original licenses. Related records: preregistration and pre-execution code, DOI 10.5281/zenodo.21701846; preprint, DOI 10.5281/zenodo.21705010. Archive SHA-256: 9628f6c68ffea9d0dd703725ac244badecf8cf867ef00a5c7d80bc5b87a8363b.