{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T20:19:31Z","timestamp":1773346771381,"version":"3.50.1"},"reference-count":0,"publisher":"Georg Thieme Verlag KG","issue":"04","license":[{"start":{"date-parts":[[2019,9,11]],"date-time":"2019-09-11T00:00:00Z","timestamp":1568160000000},"content-version":"vor","delay-in-days":41,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Appl Clin Inform"],"published-print":{"date-parts":[[2019,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>\n          Background\u2003High-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.<\/jats:p><jats:p>\n          Objectives\u2003To 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.<\/jats:p><jats:p>\n          Methods\u2003Based 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.<\/jats:p><jats:p>\n          Results\u2003The 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.<\/jats:p><jats:p>\n          Conclusion\u2003A 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.<\/jats:p>","DOI":"10.1055\/s-0039-1695793","type":"journal-article","created":{"date-parts":[[2019,9,11]],"date-time":"2019-09-11T23:08:04Z","timestamp":1568243284000},"page":"679-692","source":"Crossref","is-referenced-by-count":17,"title":["Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC"],"prefix":"10.1055","volume":"10","author":[{"given":"Sebastian","family":"Mate","sequence":"additional","affiliation":[{"name":"Medical Centre for Information and Communication Technology, Universit\u00e4tsklinikum Erlangen, Erlangen, Germany"}]},{"given":"Marvin","family":"Kampf","sequence":"additional","affiliation":[{"name":"Medical Centre for Information and Communication Technology, Universit\u00e4tsklinikum Erlangen, Erlangen, Germany"}]},{"given":"Wolfgang","family":"R\u00f6dle","sequence":"additional","affiliation":[{"name":"Chair of Medical Informatics, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg (FAU), Erlangen, Germany"}]},{"given":"Stefan","family":"Kraus","sequence":"additional","affiliation":[{"name":"Chair of Medical Informatics, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg (FAU), Erlangen, Germany"}]},{"given":"Rumyana","family":"Proynova","sequence":"additional","affiliation":[{"name":"Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany"}]},{"given":"Kaisa","family":"Silander","sequence":"additional","affiliation":[{"name":"Genomics and Biobank Unit, Finnish National Institute for Health and Welfare, Helsinki, Finland"}]},{"given":"Lars","family":"Ebert","sequence":"additional","affiliation":[{"name":"Federated Information Systems, German Cancer Research Center, Heidelberg, Germany"}]},{"given":"Martin","family":"Lablans","sequence":"additional","affiliation":[{"name":"Federated Information Systems, German Cancer Research Center, Heidelberg, Germany"}]},{"given":"Christina","family":"Sch\u00fcttler","sequence":"additional","affiliation":[{"name":"Chair of Medical Informatics, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg (FAU), Erlangen, Germany"}]},{"given":"Christian","family":"Knell","sequence":"additional","affiliation":[{"name":"Medical Centre for Information and Communication Technology, Universit\u00e4tsklinikum Erlangen, Erlangen, Germany"}]},{"given":"Niina","family":"Eklund","sequence":"additional","affiliation":[{"name":"Genomics and Biobank Unit, Finnish National Institute for Health and Welfare, Helsinki, Finland"}]},{"given":"Michael","family":"Hummel","sequence":"additional","affiliation":[{"name":"Institute of Pathology, Charit\u00e9-Universit\u00e4tsmedizin Berlin, Berlin, Germany"},{"name":"Biobanking and BioMolecular Resources Research Infrastructure (BBMRI-ERIC), Graz, Austria"}]},{"given":"Petr","family":"Holub","sequence":"additional","affiliation":[{"name":"Biobanking and BioMolecular Resources Research Infrastructure (BBMRI-ERIC), Graz, Austria"}]},{"given":"Hans-Ulrich","family":"Prokosch","sequence":"additional","affiliation":[{"name":"Medical Centre for Information and Communication Technology, Universit\u00e4tsklinikum Erlangen, Erlangen, Germany"},{"name":"Chair of Medical Informatics, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg (FAU), Erlangen, Germany"}]}],"member":"194","published-online":{"date-parts":[[2019,9,11]]},"container-title":["Applied Clinical Informatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.thieme-connect.de\/products\/ejournals\/pdf\/10.1055\/s-0039-1695793.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,12,18]],"date-time":"2019-12-18T12:05:48Z","timestamp":1576670748000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.thieme-connect.de\/DOI\/DOI?10.1055\/s-0039-1695793"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,8]]},"references-count":0,"journal-issue":{"issue":"04","published-online":{"date-parts":[[2019,8,7]]},"published-print":{"date-parts":[[2019,8]]}},"URL":"https:\/\/doi.org\/10.1055\/s-0039-1695793","relation":{},"ISSN":["1869-0327"],"issn-type":[{"value":"1869-0327","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8]]}}}