Sustainability of data
Translational Medicine Data catalogue - A comprehensive and informative list of datasets
This catalogue lists available Translational Medicine datasets, coming from academic and industry research projects as well as from clinical cohorts and genome consortia, and provides additional information, i.e. curated and standardized meta-data, about them. This catalogue will help users find information and discover resources. Researchers in Europe and worldwide can use it as a search engine to look for specific datasets. Datasets are identified by relevant criteria to facilitate browsing and the catalogue also specifies where the datasets are hosted.
ELIXIR-LU hosts the meta-data and the querying interface for the catalogue, as well as content updates and further development of the system. The Node supports the data providers in the curation of metadata and implements protocols as well as recommendation to facilitate their curation and standardisation.
eTRIKS/ELIXIR-LU Data Catalogue
This catalogue centralizes curated and standardized meta-data for ongoing and past Innovative Medicines Initiative (IMI) projects. It aims to implement the FAIR Data Principles (Findable, Accessible, Interoperable, and Re-usable) for translation medicine datasets. ELIXIR-LU works in close collaboration with IMI and eTRIKS for the initial setup and metadata collection of IMI projects.
Data integrated storage and archiving – Repository for translational datasets
Sustainable and accessible data
The node provides integrated storage and archiving for curated Translational Medicine data. Data are stored on tranSMART* servers or other suitable servers hosted by ELIXR-LU.
This service aims to keep the dataset easy to find and easy to access.
Integrated multidimensional data
Datasets comprising clinical/pre-clinical data (anonymised patient data, biological sample associated information), multi-omics (high-throughput molecular readouts from the samples) and imaging data will be integrated to systems like tranSMART. Datasets needs to be curated by the data provider and validated by the Node data quality control team before being stored at the node service platforms.
* TranSMART is a database service for handling large biomedical datasets maintained by the tranSMART foundation.
Data sharing platforms – Exploration platforms to make the most of available data
ELIXIR-LU provides platforms and protocols so that the users can gain access to the data stored at the Node. Those solutions offer different way to explore the datasets and to obtain different depths of information about the data.
As per ELIXIR policy, the data hosted by the Node are accessible to all but can remain privileged (and stored on dedicated servers) for a short time during the development phase of a project. This trial period is normally 18 months long at most.
ELIXIR supports three different access levels: public access, restricted access and special request access based on data access policy. For restricted and special request access, a data access committee needs to give the final approval before the user can obtain the dataset.
Three options to explore datasets:
1/ tranSMART – Data-sharing platform for clinical and translational research
Users can explore, analyse and visualise the available datasets. Thanks to easy browsing, selection and visualisation tools, they can choose data relevant for their respective research questions within a study but also across different projects or cohorts. Built-in analytical tools and the capability to use external workflows allow for various exploratory analyses.
2/ EGA local – Luxembourg branch of the European Genome-phenome Archive
The European platform
The European Genome-phenome Archive (EGA) allows users to explore datasets from genomic studies (personally identifiable genetic and phenotypic data resulting from biomedical research projects). Studies and datasets can be browsed on the public website and information about the aim, the experiments and the data are available.
The national branch
ELIXIR-LU will host a national instance of EGA for datasets that fits the EGA framework but for which across border restrictions apply. Users will be able to explore those local datasets through the Node’s platform or via the federated meta-data search provided by ELIXIR hub. It will provide additional information and act as an intermediary layer between the metadata from the catalogue and the actual data.
ELIXIR-LU is also working towards a national mirror of other EGA instances and will be able to help researchers with access to datasets from other countries. The Node will be able to speed up the distribution of those datasets when needed, in agreement with the other instance involved.
3/ BEACON - Data sharing protocols
With a beacon, an open web service which provides consent-based access to genomic data, researchers can browse through databases and look for genomes with specific characteristics on any chromosome. The ELIXIR Beacon implementation is available to find variants in genomic and clinical data stored at the node.
A beacon is designed to mitigate the risks associated with human genomic data sharing (data protection and privacy issues) and to be easily implemented. Each user has different access rights depending on his status, in accordance with the need for data protection in this field. ELIXIR-LU uses access levels and restrictions defined by the ELIXIR Beacon working group.
Support for the Luxembourgish Translational Medicine research programmes
ELIXIR-LU provides IT solutions for national research programmes which includes:
- electronic data capture systems to digitalize and standardize data generated by those studies (e.g. electronic case report forms utilizing REDCap)
- hosting infrastructures
- providing training for data curation, integration and analysis