Locator - a powerful tool to enhance visibility and findability of samples and data in Europe’s biobanks

This article is 912 words, an approximate five-minute read.

A biomedical treasure hunt across Europe with the right tool(s)

Over the last 50 years, medical institutions across Europe have curated biobanks to conserve collected biological samples. By using Locator, these once disparate collections can now be discovered and their samples accessed for new research.

Tissue samples from cancer patients, blood samples, or genomic data are not only needed for medical diagnosis but can be crucial for research projects, even years after the samples have been collected. These biomedical treasures not only have to be stored safely but need to be visible and easily accessible for the research community. A recent article authored by members of the German Biobank Node – GBN (BBMRI.de) focuses the development of the Locator tool as a community-based effort to enhance visibility and findability of biological samples stored in Europe’s biobanks.

Development of the Locator tool – A community-driven success story

Biological samples and associated personal information represent highly sensitive data. Thus, development of IT tools that allow researchers to search for specific types of samples categorised according to diagnosis, age, gender or other parameters, is not only a technical challenge, but also tightly connected to legal and ethical considerations.

Locator started as a national project to make biobanks across Germany searchable via one secure access portal. Now, five years later, Locator is a powerful tool building an even more connected European research landscape. A quote from the article summarises the potential of Locator:

“The infrastructure enhances the visibility, discoverability, and accessibility of biosamples within academic biobanks while upholding the security and sovereignty of biobanks’ data.” (Engels et al., 2024)

Development of the Locator is led by the German Cancer Research Centre (DKFZ) and was initially co-developed as Sample Locator with members of the German Biobank Alliance. Early-on, the team highlighted the vast potential of tightly cooperating with the wider BBMRI-ERIC research infrastructures to broaden the shared goal of facilitating cutting-edge biosample-based research across Europe.

The team made it a key strategic priority to grow an open-source community enabling tailoring the tool to both biobanking and scientific researcher communities’ needs. Part of this meant building on the existing “Samply/Bridgehead” technology from the German Cancer Consortium (DKTK), and in turn contributing many improvements to their public open-source software repositories. As explained by Martin Lablans, Head of Development at DKFZ:

“The commitment to open-source software and open data standards has proven to be a key factor in connecting research communities. Today, the same technology is used with many data types, query languages in many more consortia, and everyone is contributing to the same technology.”

Further, this cooperative approach is a long-term mechanism to maintain the tool and expand its use across borders. Now, the Locator tool helps to connect more European biobanks under the umbrella of BBMRI-ERIC’s Federated Platform. It makes Locator a true community-driven success story. This is underscored by BBMRI-ERIC’s CIO Petr Holub, who highlights the importance of the tool for the Federated Platform approach:

“The Locator tool has become a vital component of the Federated Platform – the only solution that is open-source, and which provides a very simple interface for non-technical medical researchers.”

A quick practical primer to the Locator tool (accessed via the BBMRI-ERIC website)

Locator lives up to its name by enabling a researcher to locate suitable samples and data within heterogenous biobanks in real time by searching at donor and/or sample level.

The graphical user interface is designed to be easily accessible for non-technical medical researchers. Ongoing community efforts for standardisation of sample and data categorisation allows detailed searches combining multiple criteria such as ICD-10 diagnosis, age and gender.

The image shows results from a Locator search for “C91.0 – Acute Lymphoblastic Leukaemia”, with this example containing both the ICD-10 classification code as well as the name of the disease.

After real-time communicating the query to the local biobanks (via gateway architecture), Locator informs users within seconds which biobanks contain suitable samples. Additionally, Locator provides comprehensive statistical information about age, gender distribution or tissue types.

Thus, the tool not only helps researchers find samples, but also provides crucial information needed to evaluate whether these samples represent a suitable dataset for a specific research project.

To ensure an efficient workflow for both researchers and biobanks, users can then directly request access to the samples via the connected BBMRI-ERIC Negotiator tool which forwards the request to the respective biobank. Together, these tools ensure that samples and data can not only easily be located by researchers but can also only be accessed in a secure manner respecting the rights of the original donors and biobanks.

Connecting Europe – How your biobank can become part of a secure, interconnected IT infrastructure

BBMRI-ERIC Member States share the goal to interconnect biobanks across the continent to make their samples visible and findable. BBMRI-ERIC and its partners aim to further develop and expand highly interoperable federated data infrastructures. The term federated highlights that individual biobanks act as independent nodes inside a connected network, in contrast to a fully centralised system.

To become part of this network, local biobanks form so-called ‘bridgeheads’ as part of the decentralised search architecture. They retrieve and process centrally placed search queries and send back aggregated, privacy protected, results.

If you are interested in joining your biobank to this network, you can contact federated-platform@helpdesk.bbmri-eric.eu. A technical implementation guide for the required IT architecture is provided by the German Biobank Node (resource below).

Resources

• Video guide to use the locator on the BBMRI-ERIC website
• PDF guide for the Locator
• Sample Locator via GBN/BBMRI.de:
• The sample locator: A federated search tool for biosamples and associated data in Europe using HL7 FHIR, by Engels et al, 2024
• Usability study, by Schüttler et al., 2020
• Federated Open-Source IT-development Schüttler et. al 2021
• Implementation guide (Github)