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CC BY-NC-ND 4.0 · Methods Inf Med
DOI: 10.1055/s-0044-1786839
Original Article

Europe's Largest Research Infrastructure for Curated Medical Data Models with Semantic Annotations

Sarah Riepenhausen
1   Institute of Medical Informatics, University of Münster, Münster, Nordrhein-Westfalen, Germany
,
Max Blumenstock
2   Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
,
Christian Niklas
2   Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
,
Stefan Hegselmann
1   Institute of Medical Informatics, University of Münster, Münster, Nordrhein-Westfalen, Germany
,
Philipp Neuhaus
1   Institute of Medical Informatics, University of Münster, Münster, Nordrhein-Westfalen, Germany
,
Alexandra Meidt
1   Institute of Medical Informatics, University of Münster, Münster, Nordrhein-Westfalen, Germany
,
Cornelia Püttmann
1   Institute of Medical Informatics, University of Münster, Münster, Nordrhein-Westfalen, Germany
,
Michael Storck
1   Institute of Medical Informatics, University of Münster, Münster, Nordrhein-Westfalen, Germany
,
Matthias Ganzinger
2   Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
,
Julian Varghese
1   Institute of Medical Informatics, University of Münster, Münster, Nordrhein-Westfalen, Germany
,
Martin Dugas
2   Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
3   European Research Center for Information Systems (ERCIS), Münster, Nordrhein-Westfalen, Germany
› Author Affiliations Funding This work was supported by German Research Foundation (Deutsche Forschungsgemeinschaft, DFG grants DU 352/11-1, DU 352/11-2, DU 352/14-4).
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Abstract

Background Structural metadata from the majority of clinical studies and routine health care systems is currently not yet available to the scientific community.

Objective To provide an overview of available contents in the Portal of Medical Data Models (MDM Portal).

Methods The MDM Portal is a registered European information infrastructure for research and health care, and its contents are curated and semantically annotated by medical experts. It enables users to search, view, discuss, and download existing medical data models.

Results The most frequent keyword is “clinical trial” (n = 18,777), and the most frequent disease-specific keyword is “breast neoplasms” (n = 1,943). Most data items are available in English (n = 545,749) and German (n = 109,267). Manually curated semantic annotations are available for 805,308 elements (554,352 items, 58,101 item groups, and 192,855 code list items), which were derived from 25,257 data models. In total, 1,609,225 Unified Medical Language System (UMLS) codes have been assigned, with 66,373 unique UMLS codes.

Conclusion To our knowledge, the MDM Portal constitutes Europe's largest collection of medical data models with semantically annotated elements. As such, it can be used to increase compatibility of medical datasets and can be utilized as a large expert-annotated medical text corpus for natural language processing.

Keywords

data model - semantic annotation - metadata - repository - information systems - interoperability - EDC - EHR

Authors' Contribution

S.R.: manuscript writing, statistics, revision, (supervision of) data model creation and annotation, research of available data models. M.B.: software development, revision, export of metadata and code. C.N.: revision, supervision of data model creation and annotation, research of available data models. S.H.: software architecture and development. P.N.: software development and supervision thereof, revision, export of metadata and code. A.M.: project management, dissemination concept, writing, and revision. C.P.: data model creation and annotation, research of available data models. M.S.: software development and supervision thereof. M.G.: software development and supervision thereof. J.V.: software development, writing and revision, (supervision of) data model creation and annotation, research of available data models. M.D.: Principal Investigator of MDM portal, conceptualization, selection of data models, supervision of software development, manuscript writing.




Publication History

Received: 21 October 2021

Accepted: 29 March 2024

Article published online:
13 May 2024

© 2024. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. (https://creativecommons.org/licenses/by-nc-nd/4.0/)

Georg Thieme Verlag KG
Stuttgart · New York

 

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