Journal Article

DKFZ-2019-02225

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC.

Mate, S. ; Kampf, M. ; Rödle, W. ; Kraus, S. ; Proynova, R.DKFZ* ; Silander, K. ; Ebert, L.DKFZ* ; Lablans, M.DKFZ* ; Schüttler, C. ; Knell, C. ; Eklund, N. ; Hummel, M. ; Holub, P. ; Prokosch, H.-U.

2019
Schattauer Stuttgart

This record in other databases:  

Please use a persistent id in citations: doi:10.1055/s-0039-1695793

Abstract: High-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. To 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. Based 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. The 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. A 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.

---

Contributing Institute(s):

1. Medizinische Informatik in der Translationalen Onkologie (E240)
2. Verbundinformationssysteme (E260)

Research Program(s):

1. 315 - Imaging and radiooncology (POF3-315) (POF3-315)

Appears in the scientific report 2019

---

Database coverage:
; Clarivate Analytics Master Journal List ; IF < 5 ; JCR ; PubMed Central ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

---