Auditing the Human BioMolecular Atlas Program (HuBMAP) Human Reference Atlas (HRA): An Evaluation of Core Digital Objects

Independent third-party audits of large-scale biomedical reference infrastructures remain rare, despite their potential to strengthen data quality, reproducibility, and user trust. This paper presents the first such audit of the Human Reference Atlas (HRA), produced by the Human BioMolecular Atlas Program. The HRA is a multi-format resource that includes anatomical structures, cell types, and biomarkers (ASCT+B) tables, two-dimensional (2D) Functional Tissue Unit (FTU) illustrations, three-dimensional (3D) reference objects, and Organ Mapping Antibody Panels (OMAPs). Conducted iteratively between March 2024 and August 2025, the audit examined data quality, internal consistency, and alignment with Standard Operating Procedures (SOPs). Using a mixed-methods approach that combined spreadsheet-based validation, metadata analysis, and qualitative visual review, 34 ASCT+B tables, 22 2D FTU illustrations, 30 3D reference objects, and 21 OMAP data sets were assessed. The HRA shows strong alignment with its published standards and SOPs, achieving an overall compliance rate of 94.7 per cent across all four digital object types. Structural discontinuities were limited to 3 of 34 ASCT+B tables (8.8 per cent), and all documented issues were addressed in HRA version 2.3. Beyond these findings, the study contributes a transferable four-component framework for third-party data audits: SOP-to-checklist operationalization, formula-based consistency checks, tiered compliance assessment, and iterative feedback loops. We argue that independent auditing should become standard practice in digital curation as a means of strengthening accountability for publicly funded scientific infrastructures.