Tier 2 definitions

Here we describe all the internal resources that have to do with Tier 2 and a small description of their functionality.

What is Tier 2

HCA Tier 2 metadata are sets of biological metadata, specific for each bionetwork. Genetic Diversity Tier 2 will be requested by all bionetworks to record the coverage of the atlases and survey the diversity of samples used to build the atlases. Ingestion of tier 2 is the responsibility of Data Repository (EBI), while HCA Tier 1 metadata that is going to be ingested by Data Repository (Clever Canary).

How is Tier 2 defined?

Via communications between EBI team and bionetwork coordinators who suggest relevant metadata. The EBI team is responsible for harmonising and aligning among different bionetworks where similar fields are suggested; and standardising metadata where possible through controlled vocabularies and ontologies.

What is the format?

We now have various formats for Tier 2 metadata depending on who’s the end user.

• Metadata definitions (example)
• Metadata template (example)
• Metadata recommendations (example)

  Definitions

  Based on the HCA Tier 1 definitions example, we capture all the information needed to describe each metadata field. This is intended for users who want to review Tier 2 metadata and is also the basis for extending the current HCA json schema.

  Template

  This is the sheet that we will ask contributors to fill in. This can later be integrated with Tier 1 into a full metadata DCP ingestible sheet. For help with converting t1 to dcp see https://github.com/ebi-ait/hca-tier1-to-dcp

  Recommendations

  This is a work in progress sheet intended for communications with the bionetwork to prompt them to provide more information beyond just a list of metadata field names. All such sheets are now not in use nor actively updated.