Conceptual design of a generic data harmonization process for OMOP common data model
Abstract Background To gain insight into the real-life care of patients in the healthcare system, data from hospital information systems and insurance systems are required. Consequently, linking clinical data with claims data is necessary. To ensure their syntactic and semantic interoperability, the...
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | BMC Medical Informatics and Decision Making |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12911-024-02458-7 |
| _version_ | 1797274381526761472 |
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| author | Elisa Henke Michele Zoch Yuan Peng Ines Reinecke Martin Sedlmayr Franziska Bathelt |
| author_facet | Elisa Henke Michele Zoch Yuan Peng Ines Reinecke Martin Sedlmayr Franziska Bathelt |
| author_sort | Elisa Henke |
| collection | DOAJ |
| description | Abstract Background To gain insight into the real-life care of patients in the healthcare system, data from hospital information systems and insurance systems are required. Consequently, linking clinical data with claims data is necessary. To ensure their syntactic and semantic interoperability, the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) from the Observational Health Data Sciences and Informatics (OHDSI) community was chosen. However, there is no detailed guide that would allow researchers to follow a generic process for data harmonization, i.e. the transformation of local source data into the standardized OMOP CDM format. Thus, the aim of this paper is to conceptualize a generic data harmonization process for OMOP CDM. Methods For this purpose, we conducted a literature review focusing on publications that address the harmonization of clinical or claims data in OMOP CDM. Subsequently, the process steps used and their chronological order as well as applied OHDSI tools were extracted for each included publication. The results were then compared to derive a generic sequence of the process steps. Results From 23 publications included, a generic data harmonization process for OMOP CDM was conceptualized, consisting of nine process steps: dataset specification, data profiling, vocabulary identification, coverage analysis of vocabularies, semantic mapping, structural mapping, extract-transform-load-process, qualitative and quantitative data quality analysis. Furthermore, we identified seven OHDSI tools which supported five of the process steps. Conclusions The generic data harmonization process can be used as a step-by-step guide to assist other researchers in harmonizing source data in OMOP CDM. |
| first_indexed | 2024-03-07T14:57:34Z |
| format | Article |
| id | doaj.art-828ca3572c9f4621a13519ae152bde10 |
| institution | Directory Open Access Journal |
| issn | 1472-6947 |
| language | English |
| last_indexed | 2024-03-07T14:57:34Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Informatics and Decision Making |
| spelling | doaj.art-828ca3572c9f4621a13519ae152bde102024-03-05T19:19:45ZengBMCBMC Medical Informatics and Decision Making1472-69472024-02-0124111310.1186/s12911-024-02458-7Conceptual design of a generic data harmonization process for OMOP common data modelElisa Henke0Michele Zoch1Yuan Peng2Ines Reinecke3Martin Sedlmayr4Franziska Bathelt5Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität DresdenInstitute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität DresdenInstitute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität DresdenData Integration Center, Center for Medical Informatics, University Hospital Carl Gustav Carus DresdenInstitute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität DresdenThiem-Research GmbHAbstract Background To gain insight into the real-life care of patients in the healthcare system, data from hospital information systems and insurance systems are required. Consequently, linking clinical data with claims data is necessary. To ensure their syntactic and semantic interoperability, the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) from the Observational Health Data Sciences and Informatics (OHDSI) community was chosen. However, there is no detailed guide that would allow researchers to follow a generic process for data harmonization, i.e. the transformation of local source data into the standardized OMOP CDM format. Thus, the aim of this paper is to conceptualize a generic data harmonization process for OMOP CDM. Methods For this purpose, we conducted a literature review focusing on publications that address the harmonization of clinical or claims data in OMOP CDM. Subsequently, the process steps used and their chronological order as well as applied OHDSI tools were extracted for each included publication. The results were then compared to derive a generic sequence of the process steps. Results From 23 publications included, a generic data harmonization process for OMOP CDM was conceptualized, consisting of nine process steps: dataset specification, data profiling, vocabulary identification, coverage analysis of vocabularies, semantic mapping, structural mapping, extract-transform-load-process, qualitative and quantitative data quality analysis. Furthermore, we identified seven OHDSI tools which supported five of the process steps. Conclusions The generic data harmonization process can be used as a step-by-step guide to assist other researchers in harmonizing source data in OMOP CDM.https://doi.org/10.1186/s12911-024-02458-7OMOPOHDSIInteroperabilityData harmonizationClinical dataClaims data |
| spellingShingle | Elisa Henke Michele Zoch Yuan Peng Ines Reinecke Martin Sedlmayr Franziska Bathelt Conceptual design of a generic data harmonization process for OMOP common data model BMC Medical Informatics and Decision Making OMOP OHDSI Interoperability Data harmonization Clinical data Claims data |
| title | Conceptual design of a generic data harmonization process for OMOP common data model |
| title_full | Conceptual design of a generic data harmonization process for OMOP common data model |
| title_fullStr | Conceptual design of a generic data harmonization process for OMOP common data model |
| title_full_unstemmed | Conceptual design of a generic data harmonization process for OMOP common data model |
| title_short | Conceptual design of a generic data harmonization process for OMOP common data model |
| title_sort | conceptual design of a generic data harmonization process for omop common data model |
| topic | OMOP OHDSI Interoperability Data harmonization Clinical data Claims data |
| url | https://doi.org/10.1186/s12911-024-02458-7 |
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