Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage

The Human BioMolecular Atlas Program (HuBMAP) aims to construct a reference 3D structural, cellular, and molecular atlas of the healthy adult human body. The HuBMAP Data Portal (https://portal.hubmapconsortium.org) serves experimental datasets and supports data processing, search, filtering, and visualization. The Human Reference Atlas (HRA) Portal (https://humanatlas.io) provides open access to atlas data, code, procedures, and instructional materials. Experts from more than 20 consortia are collaborating to construct the HRA's Common Coordinate Framework (CCF), knowledge graphs, and tools that describe the multiscale structure of the human body (from organs and tissues down to cells, genes, and biomarkers) and to use the HRA to understand changes that occur at each of these levels with aging, disease, and other perturbations. The 6th release of the HRA v2.0 covers 36 organs with 4,499 unique anatomical structures, 1,195 cell types, and 2,089 biomarkers (e.g., genes, proteins, lipids) linked to ontologies. In addition, three workflows were developed to map new experimental data into the HRA's CCF. This paper describes the HRA user stories, terminology, data formats, ontology validation, unified analysis workflows, user interfaces, instructional materials, application programming interface (APIs), flexible hybrid cloud infrastructure, and demonstrates first atlas usage applications and previews. ### Competing Interest Statement Core authors: Sarah A Teichmann is a remunerated member of the Scientific Advisory Boards of Qiagen, Foresite Labs and Element Biosciences, a co-founder and equity holder of TransitionBio and EnsoCell Therapeutics, and a part-time employee of GlaxoSmithKline since January 2024. HRA Team authors: Bruce J Aronow: Nexstone Immunology, Uniquity, Advisors Christopher Werlein: Speaker fee for Boehringer Ingelheim Michael Snyder: Personalis, SensOmics, Qbio, January AI, Fodsel, Filtricine, Protos, RTHM, Iollo, Marble Therapeutics, Crosshair Therapeutics, NextThought and Mirvie, Jupiter, Neuvivo, Swaza, Mitrix, Yuvan, TranscribeGlass, Applied Cognition Neil L Kelleher: Thermo Fisher Scientific, Proteinaceous, Integrated Protein Technologies, ImmPro