Pragmatic MDR: a metadata repository with bottom-up standardization of medical metadata through reuse

Abstract

Background The variety of medical documentation often leads to incompatible data elements that impede data integration between institutions. A common approach to standardize and distribute metadata definitions are ISO/IEC 11179 norm-compliant metadata repositories with top-down standardization. To the best of our knowledge, however, it is not yet common practice to reuse the content of publicly accessible metadata repositories for creation of case report forms or routine documentation. We suggest an alternative concept called pragmatic metadata repository, which enables a community-driven bottom-up approach for agreeing on data collection models. A pragmatic metadata repository collects real-world documentation and considers frequent metadata definitions as high quality with potential for reuse. Methods We implemented a pragmatic metadata repository proof of concept application and filled it with medical forms from the Portal of Medical Data Models. We applied this prototype in two use cases to demonstrate its capabilities for reusing metadata: first, integration into a study editor for the suggestion of data elements and, second, metadata synchronization between two institutions. Moreover, we evaluated the emergence of bottom-up standards in the prototype and two medical data managers assessed their quality for 24 medical concepts. Results The resulting prototype contained 466,569 unique metadata definitions. Integration into the study editor led to a reuse of 1836 items and item groups. During the metadata synchronization, semantic codes of 4608 data elements were transferred. Our evaluation revealed that for less complex medical concepts weak bottom-up standards could be established. However, more diverse disease-related concepts showed no convergence of data elements due to an enormous heterogeneity of metadata. The survey showed fair agreement (Kalpha = 0.50, 95% CI 0.43–0.56) for good item quality of bottom-up standards. Conclusions We demonstrated the feasibility of the pragmatic metadata repository concept for medical documentation. Applications of the prototype in two use cases suggest that it facilitates the reuse of data elements. Our evaluation showed that bottom-up standardization based on a large collection of real-world metadata can yield useful results. The proposed concept shall not replace existing top-down approaches, rather it complements them by showing what is commonly used in the community to guide other researchers.

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

“…The Institute of Community Medicine of the University of Greifswald extracts the UMLS annotation provided by the MDM Portal via a restful API connection for use in their own data dictionary of SHIP, 4,15 and the Medical Informatics Group of the University Hospital of Frankfurt has integrated the code suggestion function of the MDM Portal to profit from the large set of annotated elements for annotation in Samply.MDR. 8 In total, 805,308 elements with semantic annotations are available from 25,257 data models; thus the contextual meaning of diverse medical text segments is machine readable, including synonyms and complex clinically relevant concept relations.…”

“…Search functionalities are accessible through a public representational state transfer application programming interface (REST API) and, thereby, can be made available to external systems, such as a search and suggestion mechanism for semantic annotations. 10 Registered users can search, view, download, comment, edit, and upload data models.…”

“…These documents are manually transformed into ODM files with web-based tools such as ODMedit. 12 Whenever possible, tabular data or data in other formats are transformed with the help of custom R scripts or converters (for an example in Java, see Hegselmann et al 13 ). Uploads from external users are reviewed by an administrator or a moderator before public release.…”

“…In addition, these ODM files are decomposed into their components, which are stored in a second database serving as a MDR according to ISO/IEC 11179. 15 In the MDR, identical elements are only stored once. For example, data model A contains a form with item “Age” within an item group; data model B contains a different form with different item groups but has an identical item “Age.” This item “Age” is automatically assigned a unique identifier, but is linked to all instances from both data models in the MDR.…”

ELaPro, a LOINC-mapped core dataset for top laboratory procedures of eligibility screening for clinical trials

“…A direct access to the local UMLS database (2021AA) as well as the Metadata Repository (MDR) [ 58 ], the main database of the MDM portal, was granted by the Institute of Medical Informatics of the University of Muenster for the purpose of this analysis. A total of 12,027 EC forms were obtained from MDR as of August 2021, of which only 10,989 were technically accessible.…”