Supporting the Human Cell Atlas

Supporting the Human Cell Atlas

Human Cell Atlas

EMBL-EBI is a partner in the international Human Cell Atlas (HCA) initiative, which is rethinking human anatomy by defining cells according to their genetics, rather than their appearance. This global collaboration aims to create an open, accessible reference map of all cells in the healthy human body using single-cell technology.

A complete Human Cell Atlas would give us:

  • a unique ID card for each cell type
  • a three-dimensional map of how cell types work together to form tissues
  • knowledge of how all body systems are connected
  • insights into how changes in the map underlie health and disease

EMBL-EBI is working to support this unique initiative on a number of levels:

Data Coordination Platform

Alongside the Broad Institute and the University of California, Santa Cruz, EMBL-EBI has helped to develop the HCA Data Coordination Platform (HCA-DCP), the gateway to accessing data about the tens of millions of cells measured in HCA experiments.

The goals of the DCP are:

  1. Maximise the value and use of HCA data across the scientific community.
  2. Build alignment within the HCA community around a core set of computational methods and analyses.
  3. Regularly release high value single-cell data.
  4. Provide researchers access to data that will enable them to answer fundamental biological questions.
  5. Create standards for the community to use to describe single-cell experimental designs, including assay types, data and metadata.

The HCA-DCP is developed by Tony Burdett’s groups at EMBL-EBI. Tony leads the HCA-DCP project along with his counterparts Kathleen Tibbetts (Broad Institute) and Trevor Heathorn (UCSC).

For more information on the HCA-DCP work at EMBL-EBI and how we collect and standardise data, contact:
Tony Burdett – Technical Team Lead and HCA DCP co-lead

Supporting the single-cell community

The HCA-DCP provides ingestion services, which allow scientists to upload their datasets and validates the data and metadata to meet HCA standards. This process ensures HCA data are Finadable, Accessible, Interoperable and Reusable (FAIR). The data are accessible from anywhere, having been deposited in both EMBL-EBI archives and the HCA-DCP.

The HCA-DCP also provides standard analysis outputs and a platform for building tools to analyse data across sites. For example, it allows researchers to make meaningful comparisons between healthy and diseased tissues.

Explore HCA-DCP

The HCA-DCP supports this diverse community by offering new solutions for analysing and visualising single-cell data, collaboration and user/developer experience.

The goal of this platform is to minimise barriers to entry over the long term for data contribution and consumption. Over time, we will be adding features that make it easier to contribute and use data, and to develop new methods. 

Data analysis and methodology

EMBL-EBI is also involved in the analysis and development of new tools and methodologies to tackle the complex questions coming out of the HCA project.

  • Analysis Portals provide a user-friendly interface for searching, exploring and analysing the biological data collected by the HCA.
  • HCA Galaxy Instance portal contains tools for single-cell sequencing analysis and data visualisation. It offers a simple, user-friendly approach accessible through the Galaxy interface. Through this portal you can also reanalyse matrix data from the Human Cell Atlas and the EMBL-EBI Single Cell Expression Atlas.

    The HCA Galaxy Instance was developed by Irene Papatheodorou and Alvis Brazma’s groups at EMBL-EBI in collaboration with Sarah Teichmann’s group at the Wellcome Sanger Institute. The HCA Galaxy Instance infrastructure is run by the team at Freiburg University led by Björn Grüning.

For more information on the HCA Galaxy Instance contact:
Pablo Moreno – Expression Atlas Technical Coordinator

Data curation

The Samples, Phenotypes and Ontologies Team (SPOT) at EMBL-EBI is involved in ontology support for the HCA. Members of this team work with the HCA data to standardise the cell type, anatomical, and developmental stage ontology terms within the HCA database and across the EMBL-EBI databases. Research from the HCA project has also found new cell types, and the ontology terms for these are standardised with help from the colleagues listed below.

This work ensures that consistent terminology and metadata descriptions are used across biological databases. This is vital to ensure that the HCA ontologies search function works effectively, and that HCA users can easily find the data sets they need by searching by cell type or anatomical structure.

The list of sequencing data sets from the HCA project is ever growing, and so are the ontology terms. Requests for new terms can be made by opening a ticket in the HCA ontology GitHub tracker, where discussion is publicly documented.

Zoë Pendlington – Ontologist/Software Developer
David Osumi-Sutherland – Ontologist/Semantic Design
Paola Roncaglia – Ontology Consultant

Explore the HCA ontology

Scientific leadership and governance

The HCA project brings together an international community of more than 2000 researchers from over 1250 different scientific institutions around the world. Scientific leadership and steering is provided by the Organising Committee (OC), with a number of Working Groups and Biological Networks to drive specific elements of this hugely ambitious programme.

John Marioni, EMBL-EBI’s Head of Research, is a member of the HCA OC. He also co-chairs the HCA Analysis Working Group (AWG). This group organises data analysis teams, workshops and events and recommends experimental designs, analysis frameworks and best practices for the HCA. EMBL Group Leader, Oliver Stegle, also sits on the HCA AWG.

John also co-chaired the GDPR task force and, along with Laura Clarke and Tony Burdett from the Archival Infrastructure and Technology Team, and Dominik Reske (EMBL Legal),  worked on ensuring that data protection is managed appropriately in this highly collaborative environment.

Paula Frampton – Research Programme Manager - Marioni research group

Transcriptomics training

To further support the community, the EMBL-EBI Training team provides bioinformatics training on a range of relevant topics, including single-cell data analysis. To find out more visit theEMBL-EBI Training Portal.

EMBL-EBI single cell transcriptomics training courses cover a variety of topics including experimental design, data analysis, Human Cell Atlas data and metadata standards, general principles of data management, data FAIRification and best practice for generating and working with single cell RNA sequencing.

Public engagement

It is important to communicate the HCA project to a broad audience including a general public audience. EMBL-EBI is supporting the central programme of public engagement events. These events offer public audiences the opportunity to engage with HCA science and technology but also give scientists the opportunity to engage with the public's perspective and questions around their research.

A full list of the HCA public engagement activities supported by the Wellcome Genome Campus can be found on the HCA website.

Briony Jackson – Public Engagement Officer


EMBL-EBI is extremely grateful to the funders who have supported its work in the Human Cell Atlas projects.

  • Chan Zuckerberg Initiative
  • Wellcome
  • MRC
  • Horizon2020