Standardizing registry data to the OMOP Common Data Model: experience from three pulmonary hypertension databases

Abstract Background The Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) can be used to transform observational health data to a common format. CDM transformation allows for analysis across disparate databases for the generation of new, real-word evidence, which is especiall...

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Autores principales:	Patricia Biedermann, Rose Ong, Alexander Davydov, Alexandra Orlova, Philip Solovyev, Hong Sun, Graham Wetherill, Monika Brand, Eva-Maria Didden
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Pulmonary hypertension Registry Observational data Common data model Data mapping Medicine (General) R5-920
Acceso en línea:	https://doaj.org/article/16b89e782e3a40c8be239a75713ad2c8
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spelling	oai:doaj.org-article:16b89e782e3a40c8be239a75713ad2c82021-11-08T11:16:01ZStandardizing registry data to the OMOP Common Data Model: experience from three pulmonary hypertension databases10.1186/s12874-021-01434-31471-2288https://doaj.org/article/16b89e782e3a40c8be239a75713ad2c82021-11-01T00:00:00Zhttps://doi.org/10.1186/s12874-021-01434-3https://doaj.org/toc/1471-2288Abstract Background The Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) can be used to transform observational health data to a common format. CDM transformation allows for analysis across disparate databases for the generation of new, real-word evidence, which is especially important in rare disease where data are limited. Pulmonary hypertension (PH) is a progressive, life-threatening disease, with rare subgroups such as pulmonary arterial hypertension (PAH), for which generating real-world evidence is challenging. Our objective is to document the process and outcomes of transforming registry data in PH to the OMOP CDM, and highlight challenges and our potential solutions. Methods Three observational studies were transformed from the Clinical Data Interchange Standards Consortium study data tabulation model (SDTM) to OMOP CDM format. OPUS was a prospective, multi-centre registry (2014–2020) and OrPHeUS was a retrospective, multi-centre chart review (2013–2017); both enrolled patients newly treated with macitentan in the US. EXPOSURE is a prospective, multi-centre cohort study (2017–ongoing) of patients newly treated with selexipag or any PAH-specific therapy in Europe and Canada. OMOP CDM version 5.3.1 with recent OMOP CDM vocabulary was used. Imputation rules were defined and applied for missing dates to avoid exclusion of data. Custom target concepts were introduced when existing concepts did not provide sufficient granularity. Results Of the 6622 patients in the three registry studies, records were mapped for 6457. Custom target concepts were introduced for PAH subgroups (by combining SNOMED concepts or creating custom concepts) and World Health Organization functional class. Per the OMOP CDM convention, records about the absence of an event, or the lack of information, were not mapped. Excluding these non-event records, 4% (OPUS), 2% (OrPHeUS) and 1% (EXPOSURE) of records were not mapped. Conclusions SDTM data from three registries were transformed to the OMOP CDM with limited exclusion of data and deviation from the SDTM database content. Future researchers can apply our strategy and methods in different disease areas, with tailoring as necessary. Mapping registry data to the OMOP CDM facilitates more efficient collaborations between researchers and establishment of federated data networks, which is an unmet need in rare diseases.Patricia BiedermannRose OngAlexander DavydovAlexandra OrlovaPhilip SolovyevHong SunGraham WetherillMonika BrandEva-Maria DiddenBMCarticlePulmonary hypertensionRegistryObservational dataCommon data modelData mappingMedicine (General)R5-920ENBMC Medical Research Methodology, Vol 21, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Pulmonary hypertension Registry Observational data Common data model Data mapping Medicine (General) R5-920
spellingShingle	Pulmonary hypertension Registry Observational data Common data model Data mapping Medicine (General) R5-920 Patricia Biedermann Rose Ong Alexander Davydov Alexandra Orlova Philip Solovyev Hong Sun Graham Wetherill Monika Brand Eva-Maria Didden Standardizing registry data to the OMOP Common Data Model: experience from three pulmonary hypertension databases
description	Abstract Background The Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) can be used to transform observational health data to a common format. CDM transformation allows for analysis across disparate databases for the generation of new, real-word evidence, which is especially important in rare disease where data are limited. Pulmonary hypertension (PH) is a progressive, life-threatening disease, with rare subgroups such as pulmonary arterial hypertension (PAH), for which generating real-world evidence is challenging. Our objective is to document the process and outcomes of transforming registry data in PH to the OMOP CDM, and highlight challenges and our potential solutions. Methods Three observational studies were transformed from the Clinical Data Interchange Standards Consortium study data tabulation model (SDTM) to OMOP CDM format. OPUS was a prospective, multi-centre registry (2014–2020) and OrPHeUS was a retrospective, multi-centre chart review (2013–2017); both enrolled patients newly treated with macitentan in the US. EXPOSURE is a prospective, multi-centre cohort study (2017–ongoing) of patients newly treated with selexipag or any PAH-specific therapy in Europe and Canada. OMOP CDM version 5.3.1 with recent OMOP CDM vocabulary was used. Imputation rules were defined and applied for missing dates to avoid exclusion of data. Custom target concepts were introduced when existing concepts did not provide sufficient granularity. Results Of the 6622 patients in the three registry studies, records were mapped for 6457. Custom target concepts were introduced for PAH subgroups (by combining SNOMED concepts or creating custom concepts) and World Health Organization functional class. Per the OMOP CDM convention, records about the absence of an event, or the lack of information, were not mapped. Excluding these non-event records, 4% (OPUS), 2% (OrPHeUS) and 1% (EXPOSURE) of records were not mapped. Conclusions SDTM data from three registries were transformed to the OMOP CDM with limited exclusion of data and deviation from the SDTM database content. Future researchers can apply our strategy and methods in different disease areas, with tailoring as necessary. Mapping registry data to the OMOP CDM facilitates more efficient collaborations between researchers and establishment of federated data networks, which is an unmet need in rare diseases.
format	article
author	Patricia Biedermann Rose Ong Alexander Davydov Alexandra Orlova Philip Solovyev Hong Sun Graham Wetherill Monika Brand Eva-Maria Didden
author_facet	Patricia Biedermann Rose Ong Alexander Davydov Alexandra Orlova Philip Solovyev Hong Sun Graham Wetherill Monika Brand Eva-Maria Didden
author_sort	Patricia Biedermann
title	Standardizing registry data to the OMOP Common Data Model: experience from three pulmonary hypertension databases
title_short	Standardizing registry data to the OMOP Common Data Model: experience from three pulmonary hypertension databases
title_full	Standardizing registry data to the OMOP Common Data Model: experience from three pulmonary hypertension databases
title_fullStr	Standardizing registry data to the OMOP Common Data Model: experience from three pulmonary hypertension databases
title_full_unstemmed	Standardizing registry data to the OMOP Common Data Model: experience from three pulmonary hypertension databases
title_sort	standardizing registry data to the omop common data model: experience from three pulmonary hypertension databases
publisher	BMC
publishDate	2021
url	https://doaj.org/article/16b89e782e3a40c8be239a75713ad2c8
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Standardizing registry data to the OMOP Common Data Model: experience from three pulmonary hypertension databases

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