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| 001 | 144793 | ||
| 005 | 20240229112637.0 | ||
| 024 | 7 | _ | |a 10.1055/s-0039-1695793 |2 doi |
| 024 | 7 | _ | |a pmid:31509880 |2 pmid |
| 024 | 7 | _ | |a pmc:PMC6739205 |2 pmc |
| 024 | 7 | _ | |a altmetric:66608943 |2 altmetric |
| 037 | _ | _ | |a DKFZ-2019-02225 |
| 041 | _ | _ | |a eng |
| 082 | _ | _ | |a 004 |
| 100 | 1 | _ | |a Mate, Sebastian |b 0 |
| 245 | _ | _ | |a Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC. |
| 260 | _ | _ | |a Stuttgart |c 2019 |b Schattauer |
| 336 | 7 | _ | |a article |2 DRIVER |
| 336 | 7 | _ | |a Output Types/Journal article |2 DataCite |
| 336 | 7 | _ | |a Journal Article |b journal |m journal |0 PUB:(DE-HGF)16 |s 1576056290_25555 |2 PUB:(DE-HGF) |
| 336 | 7 | _ | |a ARTICLE |2 BibTeX |
| 336 | 7 | _ | |a JOURNAL_ARTICLE |2 ORCID |
| 336 | 7 | _ | |a Journal Article |0 0 |2 EndNote |
| 520 | _ | _ | |a 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. |
| 536 | _ | _ | |a 315 - Imaging and radiooncology (POF3-315) |0 G:(DE-HGF)POF3-315 |c POF3-315 |f POF III |x 0 |
| 588 | _ | _ | |a Dataset connected to CrossRef, PubMed, |
| 700 | 1 | _ | |a Kampf, Marvin |b 1 |
| 700 | 1 | _ | |a Rödle, Wolfgang |b 2 |
| 700 | 1 | _ | |a Kraus, Stefan |b 3 |
| 700 | 1 | _ | |a Proynova, Rumyana |0 P:(DE-He78)c0313b77e0c44cd2f5eb85b747c88be0 |b 4 |u dkfz |
| 700 | 1 | _ | |a Silander, Kaisa |b 5 |
| 700 | 1 | _ | |a Ebert, Lars |0 P:(DE-HGF)0 |b 6 |
| 700 | 1 | _ | |a Lablans, Martin |0 P:(DE-He78)e4ad7b4e684492de43cfcb12e5397439 |b 7 |u dkfz |
| 700 | 1 | _ | |a Schüttler, Christina |b 8 |
| 700 | 1 | _ | |a Knell, Christian |b 9 |
| 700 | 1 | _ | |a Eklund, Niina |b 10 |
| 700 | 1 | _ | |a Hummel, Michael |b 11 |
| 700 | 1 | _ | |a Holub, Petr |b 12 |
| 700 | 1 | _ | |a Prokosch, Hans-Ulrich |b 13 |
| 773 | _ | _ | |a 10.1055/s-0039-1695793 |g Vol. 10, no. 4, p. 679 - 692 |0 PERI:(DE-600)2540042-3 |n 4 |p 679 - 692 |t Applied clinical informatics |v 10 |y 2019 |x 1869-0327 |
| 909 | C | O | |p VDB |o oai:inrepo02.dkfz.de:144793 |
| 910 | 1 | _ | |a Deutsches Krebsforschungszentrum |0 I:(DE-588b)2036810-0 |k DKFZ |b 4 |6 P:(DE-He78)c0313b77e0c44cd2f5eb85b747c88be0 |
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