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. 2024 Sep 30:12:e60293.
doi: 10.2196/60293.

Toward Better Semantic Interoperability of Data Element Repositories in Medicine: Analysis Study

Zhengyong Hu #  1 , Anran Wang #  1 , Yifan Duan #  1 , Jiayin Zhou  1 , Wanfei Hu  1 , Sizhu Wu  1
Affiliations

Toward Better Semantic Interoperability of Data Element Repositories in Medicine: Analysis Study

Zhengyong Hu et al. JMIR Med Inform. .

Abstract

Background: Data element repositories facilitate high-quality medical data sharing by standardizing data and enhancing semantic interoperability. However, the application of repositories is confined to specific projects and institutions.

Objective: This study aims to explore potential issues and promote broader application of data element repositories within the medical field by evaluating and analyzing typical repositories.

Methods: Following the inclusion of 5 data element repositories through a literature review, a novel analysis framework consisting of 7 dimensions and 36 secondary indicators was constructed and used for evaluation and analysis.

Results: The study's results delineate the unique characteristics of different repositories and uncover specific issues in their construction. These issues include the absence of data reuse protocols and insufficient information regarding the application scenarios and efficacy of data elements. The repositories fully comply with only 45% (9/20) of the subprinciples for Findable and Reusable in the FAIR principle, while achieving a 90% (19/20 subprinciples) compliance rate for Accessible and 67% (10/15 subprinciples) for Interoperable.

Conclusions: The recommendations proposed in this study address the issues to improve the construction and application of repositories, offering valuable insights to data managers, computer experts, and other pertinent stakeholders.

Keywords: FAIR; ISO/IEC 11179; data element repository; metadata; semantic interoperability.

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Conflict of interest statement

Conflicts of Interest: None declared.

Figures

Figure 1
Figure 1
Flowchart of screening the data element repository for this study through literature review. The upper left gray part is the first step: searching literature from various databases. The upper right blue part is the second step: obtaining the data element repository through further screening and reading of literature. The green part below is the third step: obtaining the data element repository for this study according to the 3 inclusion and exclusion criteria: C1, C2, and C3. caDSR: Cancer Data Standards Registry and Repository; CDE: Common Data Element; CEDAR: Center for Expanded Data Annotation and Retrieval; DE: Data Element; MDM-Portal: Portal of Medical Data Model; METEOR: Metadata Online Registry; NIH: National Institutes of Health.
Figure 2
Figure 2
The analysis framework constructed in this study. The 7 light-colored parts represent the 7 analysis dimensions, and the dark rectangle in the middle is the specific indicator of each dimension. FAIR: Findable, Accessible, Interoperable, and Reusable.
Figure 3
Figure 3
Visualization of FAIR (Findable, Accessible, Interoperable, and Reusable) practices in 5 repositories, with practices divided into 4 levels: complies completely, complies partly, fails to comply, and unclear. Detailed subprinciples of FAIR are shown in Multimedia Appendix 2. caDSR: Cancer Data Standards Registry and Repository; CDE: Common Data Element; CEDAR: Center for Expanded Data Annotation and Retrieval; MDM: medical data model; METEOR: metadata online registry; NIH: National Institutes of Health.
Figure 4
Figure 4
Statistics on the practice of FAIR (Findable, Accessible, Interoperable, and Reusable) principles based on Figure 3. (A) The figure starts from the perspective of FAIR principles and horizontally counts the practice of the 4 subprinciples in Figure 3. (B) The figure starts from the perspective of data element repositories and vertically counts the practice of FAIR principles in each repository in Figure 3. caDSR: Cancer Data Standards Registry and Repository; CDE: Common Data Element; CEDAR: Center for Expanded Data Annotation and Retrieval; MDM: medical data model; METEOR: metadata online registry; NIH: National Institutes of Health.
See this image and copyright information in PMC

References

    1. Schofield PN, Bubela T, Weaver T, Portilla L, Brown SD, Hancock JM, Einhorn D, Tocchini-Valentini G, Hrabe de Angelis M, Rosenthal N, CASIMIR Rome Meeting participants Post-publication sharing of data and tools. Nature. 2009 Sep 10;461(7261):171–3. doi: 10.1038/461171a. https://europepmc.org/abstract/MED/19741686 461171a - DOI - PMC - PubMed
    1. Dugas M, Hegselmann S, Riepenhausen S, Neuhaus P, Greulich L, Meidt A, Varghese J. Compatible data models at design stage of medical information systems: leveraging related data elements from the MDM portal. Stud Health Technol Inform. 2019 Aug 21;264:113–117. doi: 10.3233/SHTI190194.SHTI190194 - DOI - PubMed
    1. Courtot M, Cherubin L, Faulconbridge A, Vaughan D, Green M, Richardson D, Harrison P, Whetzel PL, Parkinson H, Burdett T. BioSamples database: an updated sample metadata hub. Nucleic Acids Res. 2019 Jan 08;47(D1):D1172–D1178. doi: 10.1093/nar/gky1061. https://europepmc.org/abstract/MED/30407529 5165182 - DOI - PMC - PubMed
    1. Vempati Ud, Chung C, Mader C, Koleti A, Datar N, Vidović D, Wrobel D, Erickson S, Muhlich Jl, Berriz G, Benes Ch, Subramanian A, Pillai A, Shamu Ce, Schürer Stephan C. Metadata standard and data exchange specifications to describe, model, and integrate complex and diverse high-throughput screening data from the Library of Integrated Network-based Cellular Signatures (LINCS) J Biomol Screen. 2014 Jun;19(5):803–816. doi: 10.1177/1087057114522514. https://europepmc.org/abstract/MED/24518066 1087057114522514 - DOI - PMC - PubMed
    1. Pacheco AGC, Krohling RA. An attention-based mechanism to combine images and metadata in deep learning models applied to skin cancer classification. IEEE J Biomed Health Inform. 2021 Sep;25(9):3554–3563. doi: 10.1109/JBHI.2021.3062002. - DOI - PubMed

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