EGA Metadata API

Programmatically retrieve metadata from the European Genome-phenome Archive
All metadata objects generated within the European Genome-phenome Archive can be retrieved programmatically by using this API. Any user downloading omics data their genotoxicity or related studies can easily access information about samples, sequencing and experimentation.

For end-users
Type:
Application, Service
API Type:
REST
Categories:
Omics database, API Definitions for OpenRiskNet applications and data
Applicability domain:
Bioinformatics
Topic:
Information extraction
Biological area:
Omics
Targeted industry:
Other consumer products, Drugs
Targeted users:
Researchers
Relevant OpenRiskNet case study:
TGX - Toxicogenomics-based prediction and mechanism identification
Support contact:

Provided by:
Centre for Genomic Regulation
Login required:
No
Implementation status:
Application programming interface available
Technology readiness level:
TRL 9 – actual system proven in operational environment (competitive manufacturing in the case of key enabling technologies; or in space)
Integration status:
Integration in progress
Service integration operations completed:
Utilises the OpenRiskNet APIs to ensure that each service is accessible to our proposed interoperability layer.
Is annotated according to the semantic interoperability layer concept using defined ontologies.
Is containerised for easy deployment in virtual environments of OpenRiskNet instances.
Has documented scientific and technical background.
Is deployed into the OpenRiskNet reference environment.
Is listed in the OpenRiskNet discovery services.
Is listed in other central repositories like eInfraCentral, bio.tools and TeSS (ELIXIR).
Provides legal and ethical statements on how the service can be used.

Resources & Training

Report
Compute and data federation (Deliverable 2.5)
Evan Floden, Audald Lloret-Villas, Paolo Di Tommaso (CRG), Ola Spjuth (UU), Lucian Farcal (EwC), Tim Dudgeon (IM), Danyel Jennen (UM)
25 Jun 2019
Abstract:
This report details the work involved in the federation of compute and data resources between the OpenRiskNet e-infrastructure and external resources. The reference environment has been designed to be capable of handling the majority of requirements for users’ wishes to deploy and run services. However specific situations demand solutions where either the computation, the data or both reside outside the OpenRiskNet e-infrastructure. This deliverable is related to Tasks 2.7 (Interconnecting virtual environment with external infrastructures) and Tasks 2.8 (Federation between virtual environments). Resource intensive analyses, such as those performed in toxicogenomics, can have CPU, memory or disk requirements that cannot be assumed to be available across all deployment scenarios. Human sequencing data may have restrictions on where it can be processed and the vast quantity of this data often predicates that it is more efficient to “bring the computation to the data”. In achieving Tasks 2.7 and 2.8, we can demonstrate how the virtual environment can utilise external infrastructure including commercial cloud providers and data stores.
Related services:
EGA Beacon
EGA Metadata API

Target audience: Researchers, Data managers, Data owners, Data modellers, Bioinformaticians, Data providers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC, CRG, UM, UU, IM
Report