Federated EGA


Overview

The EGA project is currently a collaboration between EMBL-EBI and the CRG, regulated by agreements between the two institutions. The Federated European Genome-phenome Archive (EGA) will be a distributed network of repositories for sharing human -omics data and phenotypes. Typically a node would be an organization or project that hosts human genetic data so that the data can remain within a jurisdiction. Federated EGA gathers metadata of -omics data collections stored in national or regional archives and makes them discoverable across the EGA network.

EGA is contributing the Federated EGA model, requirements and experiences to several communities and projects like GA4GH, ELIXIR Federated Human Data Implementation Study or ELIXIR Federated Human Data community.


Documentation


  Title   Version   Description
Structure and Organization
EGA Federation: Structure and Organization 1.1 The structure of an EGA federated network and service expectations. We organise the EGA into three types of nodes: Central EGA, Federated EGA nodes and EGA Community nodes; we outline the goals of such an organization, and summarize the commitments and services provided by the nodes.
Strategic Committee
EGA Federation Strategic Committee 1.0 In the EGA Federation Strategic Committee terms of reference document we describe the purpose and objectives of the committee, which is to provide direction and strategic planning for the federated EGA project. The committee receives input from the EGA Strategic Committee and provides feedback for the EGA strategic roadmap.
Operations Committee
EGA Federation Operations Committee 1.0 The EGA Federation Operations Committee terms of reference describes the purpose and objectives of the operations committee, which is to review operational performance and coordinate technical implementation roadmaps of EGA Federated and Community nodes. The committee receives advice from the EGA Federated Strategic Committee, and provides operational reporting to the EGA Federated Strategic Committee
Guidelines
Node Operations guidelines 1.0 The EGA Federated Node Operations gives an overview of the operational areas which require resources in order to create a federated EGA node. The document is based on more than 10 years experience of establishing and operating the EBI and CRG Central EGA nodes. It provides a breakdown of the operational areas of responsibility into Helpdesk Services, Technical Operations, Software Development, and IT Infrastructure.


Available Software

The LocalEGA is a federated storage software for sensitive data.

Software
Main LocalEGA software Repository
Documentation
Main LocalEGA software Documentation


Local EGA Software

A portable toolkit to securely deposit and share human sensitive data - Local EGA, Mini-Symposium Federated Human Data, Elixir All Hands Meeting, 2020


Federated EGA API's

Below is a list of the GA4GH standards and APIs implemented by the Federated EGA. Visit EGA-GA4GH for the full list that are currently available or planned for implementation at EGA.


  API Name   API Purposes   Status   Supported
  Version
  EGA
  Documentation
htsgt A protocol for secure, efficient and reliable access to sequencing read and variation data Production TBD
DUO Semantically tag genomic datasets with usage restrictions, allowing them to become automatically discoverable based on a health, clinical, or biomedical researcher's authorization level or intended use. Production TBD
Researcher IDs These specify the collection of researchers that may access the dataset at any given time, and the credentials they must supply Production TBD
Refget Refget enables access to reference sequences using an identifier derived from the sequence itself. Production V1.0.0
Submission API An API to submitt metadat following the INSDC object schemas. Used for EGA submissions Production TBD swagger endpoint
Crypt4GH A file container specification enabling direct byte-level compatible random access to encrypted genetic data stored in community standards such as SAM/BAM/CRAM/VCF/BCF. Planned TBD
Beacon Discover genomic variants, individuals, and individuals Development TBD
Permissions API Get/set of permissions to EGA objects Development TBD