ELIXIR Pilot Actions for 2015

To date ELIXIR Pilot Actions have focussed on the deliverery of technical infrastructure components, interfaces and services for the ELIXIR Data, Tools, Compute and Standards infrastructure rather than on internal capacity building or training. The first priority for early 2015 is to balance the portfolio with activities that support the formation and development of national Nodes as well as establish the internal ELIXIR structures and working groups. An important outcome for ELIXIR is that the internal structures, Node interfaces are defined and well understood throughout the infrastructure with solid mechanisms for knowledge exchange and collaboration.

Webinars on the outcomes of these pilot actions will be given in due course, as part of the ongoing ELIXIR Webinar Series.

Rare Disease test case for ELIXIR Interoperability backbone

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. 

The Rare Disease Pilot is a joint initiative of the EU-funded RD-CONNECT projectBBMRI-NLBBMRI-ERIC and ELIXIR. Its aim is to create a federated infrastucture that will enable access to different rare disease repositories across Europe. ELIXIR's role is to test different technologies for the interoperability backbone, which which will feed into the rare disease use case within ELIXIR-EXCELERATE.

Genomic data management for TraIT using the EGA: Case study in submission and access integration of controlled access data with tranSMART and Galaxy to serve large European cohort studies

This TraIT-EGA pilot action will allow 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.

The goal of the pilot action is to connect TraIT's platform TranSMART with the European Genome-phenome Archive (EGA), and enable the Dutch researchers to use EGA as the long-term storage for raw data from all TraIT projects. The TraIT data stored in EGA will then be available on demand to the TraIT researchers for further analysis in a cloud service (using Galaxy workflow).

The project will also ensure that the researchers accessing the data though the cloud have the necessary EGA Data Access Committee (DAC) authorisation.

Collaboration with Global Alliance for Genomics and Health (GA4GH) on the Beacon project

The goal of the Pilot 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.

GA4GH Beacons allow researchers to discover datasets that are available through many participating institutions, providing a single point of access. Designed to be technically simple so that they can be implemented widely, beacons represent an important step towards collaborative, responsible sharing of human genomic data. An important objective is also to provide a reference implementation that will scale to support data discovery across all the ELIXIR Data Nodes.

Read more: Lighting beacons for data access in genomic research

ELIXIR interface with Research Data Alliance

The Research Data Alliance (RDA) is a world-wide effort of people working in different aspects of data science. In dozens of interest groups and working groups work is done on subjects as diverse as data citation and data archival and specific to fields such as wheat data interoperability and metabolomics. There are ~25 of these groups that have subjects that are of interest to ELIXIR.

The pilot has established an ELIXIR Bridging Interest Group, with ambassadors in each of the relevant RDA groups to update these groups on ELIXIR activities. This ensures that there is no unnecessarily duplicatation of work and that solutions can be (re)used. 

Capacity Building in Small and Medium Size ELIXIR Nodes 

Supporting the formation of ELIXIR community is one of the guiding objectives for ELIXIR in 2015.  This pilot aims to build the strategy to increase the joint competence and capacity for Nodes lacking large user community, large scale projects and big data or having short record of offered tools and services.  Through mapping projects at selected Nodes and determining areas of common interest; a joint capacity building strategy will be developed, tested and shared across the ELIXIR infrastructure.  Nodes should then benefit from mutual collaboration and in connection with well-established and more advanced Nodes they can utilize their know-how for a more rapid Node development.

Building the foundation for Data Carpentry and Software Carpentry within ELIXIR

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.

Nevertheless, funders and researchers increasingly call for enhanced, standards driven experimental annotation at the source and data sharing to maximise data reproducibility and reuse, in order to drive science and scientific discoveries.

To tackle this evident gap, this ELIXIR Pilot Action led by ELIXIR-UK with other support from other ELIXIR Nodes aims to leverage the work of the existing Software Carpentry initiative and launch the Data Carpentry initiative for ELIXIR, closely working with the existing international Data Carpentery network.