Contributing Data to the Human Cell Atlas

Overview

The following instructions are for scientists wanting to contribute datasets to the Human Cell Atlas (HCA). For data to be included in atlases, data contributors must provide the following data and metadata. The data and metadata are stored in three platforms to ensure adequate protection is provided to sensitive information (e.g. FASTQ and Tier 2 metadata) and non-personal data is more openly available. For the list of metadata fields, click here.

Data Platforms

The HCA Atlas Tracker stores matrices (in AnnData format) and Tier 1 metadata which are the core building blocks of atlases. Tier 1 metadata fields are typically ‘technical’ in nature (e.g. whether there was cell enrichment or depletion). For support creating an AnnData file, refer to this tutorial.

HCA requires FASTQ files and the Tier 2 metadata fields, which may contain personal information, to be stored on a secure but accessible storage platform.

The Cell Annotation Platform stores matrices and cell annotation metadata in a specially designed portal with features that allow members of the HCA community to jointly annotate data.

Once published, HCA Atlases and the source data that comprises them are available openly on the HCA Data Portal (this site), excluding identifiable data which are accessible through secure access platforms.

Inclusion Criteria

HCA’s Biological Networks (open networks of scientists responsible for constructing atlases) are responsible for choosing the datasets that end up in HCA atlases. Not all datasets submitted to the HCA Data Portal will ultimately form part of an atlas due to technical limitations such as data being processed using older technologies or due to Atlases focusing only on some, but not yet all, tissues.

Contributing Unpublished Data

HCA welcomes the contribution of unpublished data to atlases

HCA welcomes the contribution of unpublished data to atlases and has put in place mechanisms to protect the data prior to the publication of atlases. Importantly, contributors of unpublished data are encouraged to make their data publicly available as soon as possible, in accordance with the HCA Data Release Policy.

If the data contributors are unable or decline to do so, they must, at minimum, agree to make their data publicly available as soon as the Atlas that incorporates it is published in a peer-reviewed scientific journal.

Embargoing unpublished data

If you are contributing unpublished data, you may request that your data be “embargoed” in a private HCA data repository until the organ/tissue/system atlas you have contributed to is published. At that point, your data will be made available publicly via the HCA Data Explorer and linked to the corresponding Atlas page on the HCA Data Portal. Data contributors will be notified before their data is made public. Access to embargoed data will be restricted to HCA Data Wranglers, the corresponding Atlas integration team, and anyone else specified by the data contributor.

For more information, refer to HCA’s Unpublished Data Policy.

Protecting Managed Access Data

HCA has currently paused ingestion into the HCA managed access service.

When HCA’s managed access service recommences, data contributors can elect to protect their data using the HCA service. Access to managed access data is controlled through the HCA Data Access Committee. Scientists seeking access to these data must submit a data access request which is reviewed by the HCA Data Access Committee.

Submitting Metadata to Other Repositories

Data contributors are asked to notify HCA if biological metadata is submitted to other data repositories.