BBMRI-ERIC Launches The Federated Platform

The Federated Platform, a biobanking community driven initiative, has launched. In an EU first, it enables fine-grained findability of samples and data.

The Federated Platform includes two new tools, Finder and Locator, that researchers can use to discover biobanks and biomolecular resources based on their metadata. This includes aggregate information about donors, available data and samples, and even building virtual cohorts. Such expedited access and federated analysis are a first for European biobanks and researchers.

Deepening ethical searchability

Whilst broad searches of biobanks have been possible using BBMRI-ERIC’s Directory, the logical next step – the ability to conduct more detailed and real time searches of collections whilst maintaining privacy-preserving querying of pseudonymised data – has been a challenge. The Federated Platform is a powerful set of tools that solves this.

The Federated Platform searches means that queried data produces anonymised aggregated results. Data remains with the institution, and donor privacy is maintained, whilst making samples and data findable and simplifying accessibility.

Petr Holub, Chief Information Officer at BBMRI-ERIC, describes this in more detail:

“In the Federated Platform, pseudonymised patient data is available in the biobank, or at the source. You are not exporting the data to somewhere else. Instead, you install a connector, a component, that allows queries to come in, be processed on the data locally in the biobank, and anonymise the results. The results are aggregated across different data sources, across those different connectors that are installed at different places, and the ultimate result is provided to the researcher.”

BBMRI-ERIC has offered the Directory and Negotiator tools for some years. The addition of Finder and Locator enables coverage of a broader spectrum of data models. Finder is tailored towards clinical and population-based data while Locator focuses on sample derived data and some donor characteristics information.

Finder includes genomics data

A major achievement realised in Finder is the inclusion of over 200,000 genomes that make it possible to query genomic information and do genome-wide association studies (GWAS) and phenomena-wide association studies (PheWAS). It is possible to run queries on mutations and/or loss of expression, together with other data (including any omics data) in Observational Medical Outcomes Partnerships (OMOP) format when building virtual cohorts.

The Estonian National Biobank is an early contributor to this detailed genomic data in Finder. Andres Metsplanu, National Node Director for Estonia, said:

“It was already our early vision in BBMRI to make biobank data available across Europe. Therefore, new tools like ‘Finder’ and ‘Locator’ are an extremely important step forward.

“It took community effort to establish, but we have to keep in mind the complicated ethical and legal implications, and technical solutions, when involving many biobanks in ‘one virtual biobank’ that is searchable.

“The Federated Platform will speed up research and new discoveries in human genomics which is the prerequisite for implementing personalised medicine, early detection and prevention of disease.

“This is the path where Europe is going to offer the best health care possible. In this respect, the EU could lead the world because of existing and new biobanks. One practical example is The Genome of Europe project, home to the 1+ Million Genomes (1+MG) initiative where 500,000 new genomes shall be sequenced. Samples needed for that could come from the biobanks we already have.”

Dr Vita Rovita, National Node Director for BBMRI Latvia, has also coordinated significant genomic data within Finder. Asked about how such large amounts of genomic data will contribute to health research, she said:

“It is crucial to support scientists by enabling access to extensive data sets for their research endeavours and online systems. Ensuring the representation of available resources like BBMRI’s Finder can greatly maximise the use of genomic data for research advancement and societal benefit.

“From our Latvian National Biobank perspective, we find that representing our resources in online catalogues has helped us develop collaborations and ensured the greater use of samples and data. This increases the added value of our biobank and contributes much more to the research community.”

Built from understanding researcher needs

The Federated Platform allows the researcher to enter their specific combination of interest and then request the data and samples only from biobanks that have this combination of data or attributes. BBMRI-ERIC’s development team identified several use cases to understand the kind of innovations that will have most value to the wider community. The community have been involved in testing Finder and Locator.

Lukáš Muráň is a researcher at the Masaryk Memorial Cancer Institute in Brno. He found that:

“Both tools are of great benefit to researchers in the field of planning patient cohorts into projects and specifying the required characteristics of the samples.”

Martin Bartošík, a researcher at RECAMO, Brno, also provided early user feedback:

“I see a great potential in the Locator service to help me quickly and easily find samples that I need, especially if more biobanks will join to increase the portfolio of services.”

The launch of the Federated Platform will enable these kinds of specific searches. Once samples, data and virtual cohorts have been identified, researchers are able to contact biobanks through BBMRI-ERIC’s Negotiator to request access to these resources.

Developed to benefit biobanks

The launch of the Federated Platform also marks a significant step forward for the visibility of research and university hospital-based biobanks, many of which hold significant collections on specific diseases that are in high demand for ground breaking medical research.

This ability to conduct real time and detailed searches enhances the visibility of biobank collections. BBMRI-ERIC, through its National Nodes, is working with the European-wide biobanking community to help bring biobanks on board.

To achieve this means standardising the data, which is a challenge due to the varied, country specific, standards that exist. Radovan Tomášik, co-lead of the Federated Platform Task Force on behalf of BBMRI’s Czech Node, explains:

“This is where the full potential of the Federated Platform comes into play. The biobank, hospital or organisation stores their sample data in their different information systems. Someone at that organisation needs to sit down, look at all the different data sources of these systems to see how they can link them together and harmonise them into standard formats. This produces a data set that comprises all the searchable attributes, which allows the Federated Platform to see this data set via the biobank’s connector.

“So, it still sits in the organisation. It’s not sent to a third party, it’s still in their jurisdiction but the Federated Platform enables this data set to become discoverable in a secure way, according to multiple protocols and in a way that is acceptable by multiple experts.”

The benefit to biobanks readying their data goes beyond findability but also strengthens their sustainability. Zdenka Dudova, co-lead of the Federated Platform Task Force on behalf of German Biobank Node, outlines how:

“When biobanks are part of the Federated Platform, enabling access to their collections, they are also able to contribute to larger EU projects and other academic and industry collaborations, which brings in grant funding for the biobank. So, we also facilitate bringing money to the biobanks so they can continue to maintain their resources.”

Biobanks interested in making their collections visible on the Federated Platform can access information and next steps on a dedicated information page.

The Federated Platform is now available to all researchers via the BBMRI-ERIC Sample and Data Portal.