The aim of this Implementation Study was to use the existing, genome related datasets from the areas of clinical and population genetics, cancer genomics and nonhuman genome analysis to drive the refinement of the Global Alliance for Genomics and Health (GA4GH) data schema (documents) as well as to implement compatible example resources.

There is a lot of material to teach software development, data manipulation, etc., but much of it is scattered, disorganized, contradictory, or inaccessible because it assumes too much prior knowledge. Contrarily there is a lack of training material in biocuration and for the development of content standards (terminologies, minimum information checklists, exchange formats) and their use in e.g. annotation tools.

The goal of the project is to provide consent-based access to genomic data in the European Genome-phenome Archive (EGA, a joint project of EMBL-EBI and the CRG in Barcelona) as well as national resources in Finland, Sweden and the Netherlands by establishing GA4GH Beacons.

The project is funded through ELIXIR Hub a series of Implementation Studies. The first of these focused on establishing Beacons within ELIXIR Nodes and resulted in six ELIXIR Beacons in:

This TraIT-EGA project allowed Dutch research projects in translational medicine submit, store and access their data, using the European Genome Archive (EGA).

TraIT (Translational research IT) is a project by the Dutch Center for Translational Molecular Medicine (CTMM) to implement an IT infrastructure for translational biomedical research. It facilitates the collection, storage, analysis, sharing, and securing of the data generated in large multi-center translational research projects all across the Netherlands.

This study is associated with the ongoing work of the Rare Disease Community.

Access to multiple biological and clinical resources without too many barriers is of critical importance in the rare diseases field. Because of the low frequency in the population, combining data across registries, biobanks, and -omics databases is the single most important way of finding materials and gaining new insights. 

Marine genomics and metagenomics is still in its infancy, but is a rapidly expanding area of life science research. This study started in 2014 and has been instrumental in certain developments. 

To prevent the large-scale implementation of such studies from being disruptive (where the data production is faster than the speed users are able to analyze and interpret it) there is an urgent need to establish dedicated data management e-infrastructure and bioinformatics pipelines specialized for marine research.  

While the current data deluge creates a need for distributed data storage and replication, it is essential to enable data access through a single access interface.

Building upon the existing ELIXIR based collaboration within the EMBL-EBI in the UK and the Center for Genomic Regulation (CRG) in Spain, this project addressed limitations on computing, network bandwidth, and storage buffer areas that affected the EGA data delivery, and developed a protocol for secure data transfer from the EGA archive to CRG.

The EGA holds approximately half a petabyte of data, and this volume is growing rapidly. These data are a goldmine for biomedical researchers, and it is imperative that the archive continues to run smoothly and can grow to meet demand. This Pilot Action demonstrated how ELIXIR Nodes can support one another in expanding Europe’s bioinformatics capacity.