The NIH funds 18 Common Fund programs — each generating valuable datasets, each with its own data formats, metadata standards, and portals. Individually, they’re useful. Together, they could be transformative. The Common Fund Data Ecosystem (CFDE) was built to make that integration real.
This preprint describes the evolution, architecture, and practical outcomes of CFDE: a collaborative infrastructure that links Common Fund programs and makes their data findable, accessible, and reusable across program boundaries.
The HuBMAP Data Portal is the public face of the Human BioMolecular Atlas Program — the place where the data actually lands and where the broader research community can access it. This preprint describes the portal’s architecture, capabilities, and current scale.
As of October 2025, the portal holds 5,032 datasets spanning 22 data types across 27 organ classes from 310 donors. That’s not a static archive: it’s a queryable, visualizable, analysis-ready resource.
A reference atlas is only as useful as the coordinate system it’s built on. For the human body — with its 37 trillion cells, dozens of organs, and enormous variation across individuals — building that coordinate system from scratch is one of the most ambitious undertakings in modern biology.
This paper describes HuBMAP’s 3D Human Reference Atlas (HRA) v2.0: what it contains, how it was built, and how researchers can use it to map their own data.
The Human BioMolecular Atlas Program set out to do something audacious: map the healthy human body at single-cell resolution, across all major organs, from diverse populations, and make everything freely available to the research community.
The first phase was about building the foundation — ontologies, standardized protocols, analytical pipelines, and the infrastructure needed to support a project at this scale. That work is done. The program has now entered its production phase.
