Human Cell Atlas (HCA)

The Human Cell Atlas (HCA) is an international, open-science consortium, founded in 2016, that aims to create comprehensive reference maps of every cell type in the human body using single-cell and spatial genomics. It is not a data repository, a funder, or a formal legal entity in the way a standards body like GA4GH is — it is a distributed research collaboration, organized into national and regional networks and topic-specific Biological Networks, that publishes its data and analysis tools through the HCA Data Portal for free public reuse.

Scale and governance

The HCA was convened at a founding meeting in London in October 2016 by the Broad Institute, the Wellcome Sanger Institute, and Wellcome, with Aviv Regev and Sarah Teichmann defining the project’s initial goals and continuing to co-lead it. As of the most recent public reporting, the consortium describes itself as more than 3,600 members across 102 countries, coordinated through an Organizing Committee of roughly 35 international scientists, Executive Offices in the UK, USA, Japan, and Singapore, and dedicated Working Groups covering Analysis, Ethics, Equity, Standards, Technology, and the Data Ecosystem. Eighteen Biological Networks each focus on mapping a specific tissue or organ system (nervous system, lung, heart, intestine, immune system, and others), and Regional Networks coordinate participation across Africa, Asia, Latin America, and the Middle East.

What the HCA Data Portal provides

The HCA Data Portal is the consortium’s public access point for single-cell and spatial genomics data, computational analysis tools, and the reference atlases produced from them. Data contributed to the HCA is intended to be freely available worldwide, alongside the software used to generate and analyze it — a stated design goal of the project since its founding. This matters for research administrators for two reasons distinct from the science itself: first, when a genomics-heavy project’s data management plan proposes contributing to, or reusing data from, an HCA Biological Network, the commitment is to that network’s own metadata, protocol, and access standards, not to a generic repository deposit; second, when assessing whether a proposed atlasing project duplicates existing coverage, the HCA’s own published roadmap and completed “V1” atlases (including lung, nervous system, eye, and organoid atlases, with development, oral/craniofacial, skin, gut, musculoskeletal, liver, and adipose-tissue atlases in progress as of the most recent roadmap) are the reference point to check first.

Funding

The HCA is funded by a mix of philanthropic and public funders rather than a single grant or agency — publicly documented supporters include the Chan Zuckerberg Initiative, Wellcome, the Helmsley Charitable Trust, the UK Medical Research Council, the European Commission, the British Heart Foundation, and the Klarman Family Foundation, with individual published studies drawing on well over 100 distinct funding sources given the project’s grassroots, researcher-driven structure. A research administrator reviewing a proposal that cites HCA affiliation should expect funding attribution to this kind of distributed, multi-funder pattern rather than a single sponsoring body.

Why this matters for research data management

The HCA is a useful case study in large-scale, federated research infrastructure: it has no central funder, no single legal owner, and no mandatory participation requirement, yet it coordinates data standards, ethics review, and public access across thousands of contributing researchers through its Working Groups rather than through regulation. Where a project’s data use agreement or repository choice needs to demonstrate long-term trustworthiness, comparing the HCA Data Portal’s access model against certification frameworks such as CoreTrustSeal is a reasonable due-diligence step, since HCA participation itself is not a certification and does not substitute for one.

Examples

A university informatics office advising a PI whose proposal contributes single-cell RNA-seq data to an HCA Biological Network would reference that network’s own metadata and protocol standards in the data management plan, not a generic repository deposit policy.

A program officer assessing whether a proposed atlasing project duplicates existing work would check the HCA’s published roadmap and completed V1 atlases for the tissue in question before treating the proposal as novel.

Not the same as

A single-lab single-cell RNA-seq dataset deposited in a general-purpose repository such as GEO is not, by itself, part of the Human Cell Atlas. It becomes part of the HCA only once formally contributed to, and accepted by, one of its Biological Networks under that network’s own standards — general repository deposit and HCA membership are not interchangeable.