The sample locator: A federated search tool for biosamples and associated data in Europe using HL7 FHIR

German Biobank Alliance (GBA) IT development team

doi:10.1016/j.compbiomed.2024.108941

The sample locator: A federated search tool for biosamples and associated data in Europe using HL7 FHIR

German Biobank Alliance (GBA) IT development team

Abstract

Background: This study outlines the development of a highly interoperable federated IT infrastructure for academic biobanks located at the major university hospital sites across Germany. High-quality biosamples linked to clinical data, stored in biobanks are essential for biomedical research. We aimed to facilitate the findability of these biosamples and their associated data. Networks of biobanks provide access to even larger pools of samples and data even from rare diseases and small disease subgroups. The German Biobank Alliance (GBA) established in 2017 under the umbrella of the German Biobank Node (GBN), has taken on the mission of a federated data discovery service to make biosamples and associated data available to researchers across Germany and Europe. Methods: In this context, we identified the requirements of researchers seeking human biosamples from biobanks and the needs of biobanks for data sovereignty over their samples and data in conjunction with the sample donor's consent. Based on this, we developed a highly interoperable federated IT infrastructure using standards such as Fast Healthcare Interoperability Resources (HL7 FHIR) and Clinical Quality Language (CQL). Results: The infrastructure comprises two major components enabling federated real-time access to biosample metadata, allowing privacy-compliant queries and subsequent project requests. It has been in use since 2019, connecting 16 German academic biobanks, with additional European biobanks joining. In production since 2019 it has run 4941 queries over the span of one year on more than 900,000 biosamples collected from more than 170,000 donors. Conclusion: This infrastructure enhances the visibility and accessibility of biosamples for research, addressing the growing demand for human biosamples and associated data in research. It also underscores the need for improvements in processes beyond IT infrastructure, aiming to advance biomedical research and similar infrastructure development in other fields.

Originalsprache	Englisch
Aufsatznummer	108941
Zeitschrift	Computers in Biology and Medicine
Jahrgang	180
ISSN	0010-4825
DOIs	https://doi.org/10.1016/j.compbiomed.2024.108941
Publikationsstatus	Veröffentlicht - 09.2024

Fördermittel

Despite significant advances in IT infrastructures to support biomedical research, the visibility and accessibility of biosamples across Germany remains a motivational driver and several research gaps needed to be addressed. The German Biobank Alliance (GBA) aimed to develop a system that would allow real-time discovery of biosamples at the donor level through a user-friendly graphical interface (GUI). This development followed the FAIR principles of data sharing [9]: discoverability, accessibility, interoperability and reusability. These principles were applied not only to the biosamples, but also to their descriptive data, ensuring comprehensive data sharing and integration. During the pilot phase of the German Biobank Node (GBN) [1], a thorough requirements analysis [10] was conducted with input from various stakeholders, leading to the identification of key needs [11]. These included providing value to researchers through an intuitive query interface, securely connecting biobank data to a central search service without transferring sensitive non-aggregated data, while maintaining data sovereignty so that biobanks control their data and access requests. In addition, technical interoperability was ensured by adhering to established standards to support different biobank systems, while syntactic and semantic interoperability was achieved through common data formats and semantic codes. Sustainability was a priority, with the infrastructure being open source and well documented to facilitate widespread access and co-development. Finally, the infrastructure was designed to support existing biobank systems and workflows without imposing significant additional burdens. These measures highlight both the progress that has been made and the continuing need to address the remaining challenges in optimising biobank sample and data sharing and accessibility.Biobanks that want to take part in the GBA IT infrastructure and offer their samples through the Sample Locator can access detailed technical instructions from the BBMRI.de/GBA Implementation Guide [30]. The instructions cover the deployment and installation of the Bridgehead, which includes of the Samply.Blaze store and the Connector. For specific installation guidance, they can refer to the Bridgehead repository on GitHub [31]. Local biobanks must ensure that their server or virtual machine meets the minimum hardware requirements and supports Docker. Network communication requires outgoing HTTPS and proxy support, along with specific firewall configuration recommendations [32]. The local IT staff in the biobank or the institution then must then ensure data harmonisation via the ETL-process described above. Fig. 2a illustrates the process of extracting donor and sample data from primary sources, transforming it (A) according to the bbmri.de FHIR profile [33], and loading it (B) into the Samply.Blaze store within the local Bridgehead. The software's development, deployment, and operation are thoroughly documented [32], and the source code is published open source under the Apache-2.0 license [34]. In the following years, additional European biobanks from the BBMRI-ERIC will be joining the network, along with other German biobanks.The German Federal Ministry of Education (https://www.bmbf.de/) funded the German Biobank Alliance project (grant numbers 16EY1701-14). The German Federal Ministry of Education ( https://www.bmbf.de/ ) funded the German Biobank Alliance project (grant numbers 16EY1701-14).

Träger	Trägernummer
Federal Ministry of Education
German Federal Ministry of Education of Research
German Biobank Alliance	16EY1701-14

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10.1016/j.compbiomed.2024.108941

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title = "The sample locator: A federated search tool for biosamples and associated data in Europe using HL7 FHIR",

abstract = "Background: This study outlines the development of a highly interoperable federated IT infrastructure for academic biobanks located at the major university hospital sites across Germany. High-quality biosamples linked to clinical data, stored in biobanks are essential for biomedical research. We aimed to facilitate the findability of these biosamples and their associated data. Networks of biobanks provide access to even larger pools of samples and data even from rare diseases and small disease subgroups. The German Biobank Alliance (GBA) established in 2017 under the umbrella of the German Biobank Node (GBN), has taken on the mission of a federated data discovery service to make biosamples and associated data available to researchers across Germany and Europe. Methods: In this context, we identified the requirements of researchers seeking human biosamples from biobanks and the needs of biobanks for data sovereignty over their samples and data in conjunction with the sample donor's consent. Based on this, we developed a highly interoperable federated IT infrastructure using standards such as Fast Healthcare Interoperability Resources (HL7 FHIR) and Clinical Quality Language (CQL). Results: The infrastructure comprises two major components enabling federated real-time access to biosample metadata, allowing privacy-compliant queries and subsequent project requests. It has been in use since 2019, connecting 16 German academic biobanks, with additional European biobanks joining. In production since 2019 it has run 4941 queries over the span of one year on more than 900,000 biosamples collected from more than 170,000 donors. Conclusion: This infrastructure enhances the visibility and accessibility of biosamples for research, addressing the growing demand for human biosamples and associated data in research. It also underscores the need for improvements in processes beyond IT infrastructure, aiming to advance biomedical research and similar infrastructure development in other fields.",

author = "\{German Biobank Alliance (GBA) IT development team\} and Cecilia Engels and Jori Kern and Zdenka Dudov{\'a} and Noemi Deppenwiese and Alexander Kiel and Bj{\"o}rn Kroll and Tobias Kussel and Christina Sch{\"u}ttler and Radovan Tom{\'a}{\v s}ik and Michael Hummel and Martin Lablans and Martin Breu and David Croft and Christoph Dolch and Petra Duhm-Harbeck and Lars Ebert and C{\"a}cilia Engels and Christian Knell and Kock-Schoppenhauer, \{Ann Kristin\} and John Linde and Christian Maier and Michael Neumann and Matthias {\"O}felein and Matthias Rambow and Susanne Sahr and Florian Stampe and Deniz Tas and Hannes Ulrich and Prokosch, \{Hans Ulrich\}",

note = "Publisher Copyright: {\textcopyright} 2024 The Authors",

year = "2024",

month = sep,

doi = "10.1016/j.compbiomed.2024.108941",

language = "English",

volume = "180",

journal = "Computers in Biology and Medicine",

issn = "0010-4825",

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TY - JOUR

T1 - The sample locator

T2 - A federated search tool for biosamples and associated data in Europe using HL7 FHIR

AU - German Biobank Alliance (GBA) IT development team

AU - Engels, Cecilia

AU - Kern, Jori

AU - Dudová, Zdenka

AU - Deppenwiese, Noemi

AU - Kiel, Alexander

AU - Kroll, Björn

AU - Kussel, Tobias

AU - Schüttler, Christina

AU - Tomášik, Radovan

AU - Hummel, Michael

AU - Lablans, Martin

AU - Breu, Martin

AU - Croft, David

AU - Dolch, Christoph

AU - Duhm-Harbeck, Petra

AU - Ebert, Lars

AU - Engels, Cäcilia

AU - Knell, Christian

AU - Kock-Schoppenhauer, Ann Kristin

AU - Linde, John

AU - Maier, Christian

AU - Neumann, Michael

AU - Öfelein, Matthias

AU - Rambow, Matthias

AU - Sahr, Susanne

AU - Stampe, Florian

AU - Tas, Deniz

AU - Ulrich, Hannes

AU - Prokosch, Hans Ulrich

PY - 2024/9

Y1 - 2024/9

N2 - Background: This study outlines the development of a highly interoperable federated IT infrastructure for academic biobanks located at the major university hospital sites across Germany. High-quality biosamples linked to clinical data, stored in biobanks are essential for biomedical research. We aimed to facilitate the findability of these biosamples and their associated data. Networks of biobanks provide access to even larger pools of samples and data even from rare diseases and small disease subgroups. The German Biobank Alliance (GBA) established in 2017 under the umbrella of the German Biobank Node (GBN), has taken on the mission of a federated data discovery service to make biosamples and associated data available to researchers across Germany and Europe. Methods: In this context, we identified the requirements of researchers seeking human biosamples from biobanks and the needs of biobanks for data sovereignty over their samples and data in conjunction with the sample donor's consent. Based on this, we developed a highly interoperable federated IT infrastructure using standards such as Fast Healthcare Interoperability Resources (HL7 FHIR) and Clinical Quality Language (CQL). Results: The infrastructure comprises two major components enabling federated real-time access to biosample metadata, allowing privacy-compliant queries and subsequent project requests. It has been in use since 2019, connecting 16 German academic biobanks, with additional European biobanks joining. In production since 2019 it has run 4941 queries over the span of one year on more than 900,000 biosamples collected from more than 170,000 donors. Conclusion: This infrastructure enhances the visibility and accessibility of biosamples for research, addressing the growing demand for human biosamples and associated data in research. It also underscores the need for improvements in processes beyond IT infrastructure, aiming to advance biomedical research and similar infrastructure development in other fields.

AB - Background: This study outlines the development of a highly interoperable federated IT infrastructure for academic biobanks located at the major university hospital sites across Germany. High-quality biosamples linked to clinical data, stored in biobanks are essential for biomedical research. We aimed to facilitate the findability of these biosamples and their associated data. Networks of biobanks provide access to even larger pools of samples and data even from rare diseases and small disease subgroups. The German Biobank Alliance (GBA) established in 2017 under the umbrella of the German Biobank Node (GBN), has taken on the mission of a federated data discovery service to make biosamples and associated data available to researchers across Germany and Europe. Methods: In this context, we identified the requirements of researchers seeking human biosamples from biobanks and the needs of biobanks for data sovereignty over their samples and data in conjunction with the sample donor's consent. Based on this, we developed a highly interoperable federated IT infrastructure using standards such as Fast Healthcare Interoperability Resources (HL7 FHIR) and Clinical Quality Language (CQL). Results: The infrastructure comprises two major components enabling federated real-time access to biosample metadata, allowing privacy-compliant queries and subsequent project requests. It has been in use since 2019, connecting 16 German academic biobanks, with additional European biobanks joining. In production since 2019 it has run 4941 queries over the span of one year on more than 900,000 biosamples collected from more than 170,000 donors. Conclusion: This infrastructure enhances the visibility and accessibility of biosamples for research, addressing the growing demand for human biosamples and associated data in research. It also underscores the need for improvements in processes beyond IT infrastructure, aiming to advance biomedical research and similar infrastructure development in other fields.

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DO - 10.1016/j.compbiomed.2024.108941

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SN - 0010-4825

VL - 180

JO - Computers in Biology and Medicine

JF - Computers in Biology and Medicine

M1 - 108941

ER -

The sample locator: A federated search tool for biosamples and associated data in Europe using HL7 FHIR

Abstract

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