Integration, Cataloguing and Management of Biobanking and
Clinical Data Using FAIR Genomes Metadata Schema

J 2025

Integration, Cataloguing and Management of Biobanking and Clinical Data Using FAIR Genomes Metadata Schema

KACOVÁ, Radoslava; Tomáš HOUFEK; Ondřej HORKÝ; Radovan TOMÁŠIK; Jan KURÁŇ et al.

Základní údaje

Originální název

Integration, Cataloguing and Management of Biobanking and Clinical Data Using FAIR Genomes Metadata Schema

Autoři

KACOVÁ, Radoslava; Tomáš HOUFEK; Ondřej HORKÝ; Radovan TOMÁŠIK ; Jan KURÁŇ; Michal RŮŽIČKA; Roman HRSTKA; Vít NOVÁČEK a Zdenka DUDOVÁ

Vydání

Data Intelligence, MIT Press, 2025, 2096-7004

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Čína

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14330/25:00140839

Organizační jednotka

Fakulta informatiky

Klíčová slova anglicky

FAIR data point; FAIR principles; Metadata; Interoperability; Secondary use of healthcare data; Hospital-generated data; Genomic data; Data sharing

Štítky

bank of biological material, data management, data reusability, FAIRification, hospital data, rivok, sensitive data

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 20. 3. 2026 15:54, Mgr. Eva Špillingová

Anotace

V originále

In the dynamic environment of hospitals, valuable real-world data often remain underutilised despite their potential to revolutionize cancer research and personalised medicine. This study explores the challenges and opportunities in managing hospital-generated data, particularly within the Masaryk Memorial Cancer Institute (MMCI) in Brno, Czech Republic. Utilizing Next-Generation Sequencing (NGS) technology, MMCI generates substantial volumes of genomic data. Due to inadequate curation, these data remain difficult to integrate with clinical records for secondary use (such as personalised treatment outcome prediction and patient stratification based on their genomic profiles). This paper proposes solutions based on the FAIR principles (Findability, Accessibility, Interoperability, and Reusability) to enhance data sharing and reuse. The primary output of our work is the development of an automated pipeline that continuously processes and integrates NGS data with clinical and biobank information upon their creation. It stores the data in a special secured repository for sensitive data in a structured form to ensure smooth retrieval.

Návaznosti

EH22_008/0004644, projekt VaV

Název: Záchrana životů prostřednictvím výzkumu v oblasti včasné detekce a prevence rakoviny: Molekulární, genomické a sociální faktory

LM2023033, projekt VaV

Název: Síť českých biobank

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, BBMRI.cz - Síť českých biobank

MUNI/A/1638/2024, interní kód MU

Název: Umělá inteligence a správa komplexních rozsáhlých dat

Investor: Masarykova univerzita, Umělá inteligence a správa komplexních rozsáhlých dat

90254, velká výzkumná infrastruktura

Název: e-INFRA CZ II

Citovat

KACOVÁ, Radoslava; Tomáš HOUFEK; Ondřej HORKÝ; Radovan TOMÁŠIK; Jan KURÁŇ; Michal RŮŽIČKA; Roman HRSTKA; Vít NOVÁČEK a Zdenka DUDOVÁ. Integration, Cataloguing and Management of Biobanking and Clinical Data Using FAIR Genomes Metadata Schema. Data Intelligence. MIT Press, 2025, roč. 2025, č. 1, s. 163-184. ISSN 2096-7004. Dostupné z: https://doi.org/10.3724/2096-7004.di.2025.0005.

@article{2483758,
   author = {Kacová, Radoslava and Houfek, Tomáš and Horký, Ondřej and Tomášik, Radovan and Kuráň, Jan and Růžička, Michal and Hrstka, Roman and Nováček, Vít and Dudová, Zdenka},
   article_number = {1},
   doi = {https://doi.org/10.3724/2096-7004.di.2025.0005},
   keywords = {FAIR data point; FAIR principles; Metadata; Interoperability; Secondary use of healthcare data; Hospital-generated data; Genomic data; Data sharing},
   language = {eng},
   issn = {2096-7004},
   journal = {Data Intelligence},
   title = {Integration, Cataloguing and Management of Biobanking and Clinical Data Using FAIR Genomes Metadata Schema},
   url = {https://www.sciengine.com/DI/doi/10.3724/2096-7004.di.2025.0005},
   volume = {2025},
   year = {2025}
}

TY  - JOUR
ID  - 2483758
AU  - Kacová, Radoslava - Houfek, Tomáš - Horký, Ondřej - Tomášik, Radovan - Kuráň, Jan - Růžička, Michal - Hrstka, Roman - Nováček, Vít - Dudová, Zdenka
PY  - 2025
TI  - Integration, Cataloguing and Management of Biobanking and Clinical Data Using FAIR Genomes Metadata Schema
JF  - Data Intelligence
VL  - 2025
IS  - 1
SP  - 163-184
EP  - 163-184
PB  - MIT Press
SN  - 20967004
KW  - FAIR data point
KW  - FAIR principles
KW  - Metadata
KW  - Interoperability
KW  - Secondary use of healthcare data
KW  - Hospital-generated data
KW  - Genomic data
KW  - Data sharing
UR  - https://www.sciengine.com/DI/doi/10.3724/2096-7004.di.2025.0005
N2  - In the dynamic environment of hospitals, valuable real-world data often remain underutilised despite their potential to revolutionize cancer research and personalised medicine. This study explores the challenges and opportunities in managing hospital-generated data, particularly within the Masaryk Memorial Cancer Institute (MMCI) in Brno, Czech Republic. Utilizing Next-Generation Sequencing (NGS) technology, MMCI generates substantial volumes of genomic data. Due to inadequate curation, these data remain difficult to integrate with clinical records for secondary use (such as personalised treatment outcome prediction and patient stratification based on their genomic profiles). This paper proposes solutions based on the FAIR principles (Findability, Accessibility, Interoperability, and Reusability) to enhance data sharing and reuse. The primary output of our work is the development of an automated pipeline that continuously processes and integrates NGS data with clinical and biobank information upon their creation. It stores the data in a special secured repository for sensitive data in a structured form to ensure smooth retrieval.
ER  -

KACOVÁ, Radoslava; Tomáš HOUFEK; Ondřej HORKÝ; Radovan TOMÁŠIK; Jan KURÁŇ; Michal RŮŽIČKA; Roman HRSTKA; Vít NOVÁČEK a Zdenka DUDOVÁ. Integration, Cataloguing and Management of Biobanking and Clinical Data Using FAIR Genomes Metadata Schema. \textit{Data Intelligence}. MIT Press, 2025, roč.~2025, č.~1, s.~163-184. ISSN~2096-7004. Dostupné z: https://doi.org/10.3724/2096-7004.di.2025.0005.

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