Definitions to data flow: Operationalizing MIABIS in HL7 FHIR

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00209805%3A_____%2F25%3A00080416" target="_blank" >RIV/00209805:_____/25:00080416 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14330/25:00142739

Result on the web

<a href="https://www.sciencedirect.com/science/article/pii/S1532046425001480?via%3Dihub" target="_blank" >https://www.sciencedirect.com/science/article/pii/S1532046425001480?via%3Dihub</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.jbi.2025.104919" target="_blank" >10.1016/j.jbi.2025.104919</a>

Result language

angličtina

Original language name

Definitions to data flow: Operationalizing MIABIS in HL7 FHIR

Original language description

OBJECTIVE: Biobanks and biomolecular resources are increasingly central to data-driven biomedical research, encompassing not only metadata but also granular, sample-related data from diverse sources such as healthcare systems, national registries, and research outputs. However, the lack of a standardised, machine-readable format for representing such data limits interoperability, data reuse and integration into clinical and research environments. While MIABIS provides a conceptual model for biobank data, its abstract nature and reliance on heterogeneous implementations create barriers to practical, scalable adoption. This study presents a pragmatic, operational implementation of MIABIS focused on enabling real-world exchange and integration of sample-level data. METHODS: We systematically evaluated established data exchange standards, comparing HL7 FHIR and OMOP CDM with respect to their suitability for structuring sample-related data in a semantically robust and machine-readable form. Based on this analysis, we developed a FHIR-based representation of MIABIS that supports complex biobank structures and enables integration with federated data infrastructures. Supporting tools, including a Python library and an implementation guide, were created to ensure usability across diverse research and clinical contexts. RESULTS: We created nine interoperable FHIR profiles covering core MIABIS entities, ensuring consistency with FHIR standards. To support adoption, we developed an open-source Python library that abstracts FHIR interactions and provides schema validation for MIABIS-compliant data. The library was integrated into an ETL tool in operation at Czech Node of BBMRI-ERIC, European Biobanking and Biomolecular Resources Research Infrastructure, to demonstrate usability with real-world sample-related data. Separately, we validated the representation of MIABIS entities at the organisational level by converting the data structures of BBMRI-ERIC Directory into FHIR, demonstrating compatibility with federated data infrastructures. CONCLUSION: This work delivers a machine-readable, interoperable implementation of MIABIS, enabling the exchange of both organisational and sample-level data across biobanks and health information systems. By integrating MIABIS with HL7 FHIR, we provide a host of reusable tools and mechanisms for further evolution of the data model. Combined, these benefits can help with the integration into clinical and research workflows, supporting data discoverability, reuse, and cross-institutional collaboration in biomedical research.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2025

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of biomedical informatics

ISSN

1532-0464

e-ISSN

1532-0480

Volume of the periodical

117

Issue of the periodical within the volume

November 2025

Country of publishing house

US - UNITED STATES

Number of pages

10

Pages from-to

104919

UT code for WoS article

001593616600001

EID of the result in the Scopus database

2-s2.0-105021669070