ArticleApplied clinical informatics2019
Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC.
Article in Applied clinical informatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 2 of them syntheses that pooled it.
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Who cites it
9 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Understanding the Nature of Metadata: Systematic Review.Journal of medical Internet research · 2022Pooled it
- Guidelines for Biobanking of Bone Marrow Adipose Tissue and Related Cell Types: Report of the Biobanking Working Group of the International Bone Marrow Adiposity Society.Frontiers in endocrinology · 2021Guideline
- Article
- A comprehensive European Colorectal Cancer Cohort dataset.Scientific data · 2026Article
- A natural language processing approach to support biomedical data harmonization: Leveraging large language models.PloS one · 2025Article
- Data Management in Biobanking: Strategies, Challenges, and Future Directions.Biotech (Basel (Switzerland)) · 2024Review
- Unlocking the potential of big data and AI in medicine: insights from biobanking.Frontiers in medicine · 2024Article
- The Future of Biobanking: What Is Next?Biotech (Basel (Switzerland)) · 2020Article
- Sync for Genes: Making Clinical Genomics Available for Precision Medicine at the Point-of-Care.Applied clinical informatics · 2020Article
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh-quality clinical data and biological specimens are key for medical research and personalized medicine. The Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC) aims to facilitate access to such biological resources. The accompanying ADOPT BBMRI-ERIC project kick-started BBMRI-ERIC by collecting colorectal cancer data from European biobanks.
objectivesTo transform these data into a common representation, a uniform approach for data integration and harmonization had to be developed. This article describes the design and the implementation of a toolset for this task.
methodsBased on the semantics of a metadata repository, we developed a lexical bag-of-words matcher, capable of semiautomatically mapping local biobank terms to the central ADOPT BBMRI-ERIC terminology. Its algorithm supports fuzzy matching, utilization of synonyms, and sentiment tagging. To process the anonymized instance data based on these mappings, we also developed a data transformation application.
resultsThe implementation was used to process the data from 10 European biobanks. The lexical matcher automatically and correctly mapped 78.48% of the 1,492 local biobank terms, and human experts were able to complete the remaining mappings. We used the expert-curated mappings to successfully process 147,608 data records from 3,415 patients.
conclusionA generic harmonization approach was created and successfully used for cross-institutional data harmonization across 10 European biobanks. The software tools were made available as open source.
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