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. 2023 Sep 13:15:969-986.
doi: 10.2147/CLEP.S419481. eCollection 2023.

Transforming the Information System for Research in Primary Care (SIDIAP) in Catalonia to the OMOP Common Data Model and Its Use for COVID-19 Research

Berta Raventós #  1   2 , Sergio Fernández-Bertolín #  1 , María Aragón  1 , Erica A Voss  3   4   5 , Clair Blacketer  3   4   5 , Leonardo Méndez-Boo  6 , Martina Recalde  1 , Elena Roel  1   2 , Andrea Pistillo  1   7 , Carlen Reyes  1 , Sebastiaan van Sandijk  8 , Lars Halvorsen  9 , Peter R Rijnbeek  4   5 , Edward Burn  1   10 , Talita Duarte-Salles  1   4
Affiliations

Transforming the Information System for Research in Primary Care (SIDIAP) in Catalonia to the OMOP Common Data Model and Its Use for COVID-19 Research

Berta Raventós et al. Clin Epidemiol. .

Abstract

Purpose: The primary aim of this work was to convert the Information System for Research in Primary Care (SIDIAP) from Catalonia, Spain, to the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). Our second aim was to provide a descriptive analysis of COVID-19-related outcomes among the general population.

Patients and methods: We mapped patient-level data from SIDIAP to the OMOP CDM and we performed more than 3,400 data quality checks to assess its readiness for research. We established a general population cohort as of the 1st March 2020 and identified outpatient COVID-19 diagnoses or tested positive for, hospitalised with, admitted to intensive care units (ICU) with, died with, or vaccinated against COVID-19 up to 30th June 2022.

Results: After verifying the high quality of the transformed dataset, we included 5,870,274 individuals in the general population cohort. Of those, 604,472 had either an outpatient COVID-19 diagnosis or positive test result, 58,991 had a hospitalisation, 5,642 had an ICU admission, and 11,233 died with COVID-19. A total of 4,584,515 received a COVID-19 vaccine. People who were hospitalised or died were more commonly older, male, and with more comorbidities. Those admitted to ICU with COVID-19 were generally younger and more often male than those hospitalised and those who died.

Conclusion: We successfully transformed SIDIAP to the OMOP CDM. From this dataset, a general population cohort of 5.9 million individuals was identified and their COVID-19-related outcomes over time were described. The transformed SIDIAP database is a valuable resource that can enable distributed network research in COVID-19 and beyond.

Keywords: OMOP; common data model; electronic health records; medical ontologies; secondary data use.

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Conflict of interest statement

EAV and CB are employees of Janssen Research and Development LLC and shareholders of Johnson & Johnson (J&J) stock. LH reports edenceHealth, as a certified EHDEN SME, received payment for certifying the earlier OMOP CDM transformation work done by SIDIAP in their function as an EHDEN Data Partner, during the conduct of the study. TD-S reports grants from Innovative Medicines Initiative 2, during the conduct of the study. The authors report no other conflicts of interest in this work.

Figures

Figure 1
Figure 1
Histogram of age, stratified by sex, for the general population and each COVID-19 outcome cohort.
Figure 2
Figure 2
COVID-19 outcome cohort entry over calendar time, stratified by age group.
Figure 3
Figure 3
Symptoms recorded at time of outpatient COVID-19 diagnosis or positive test.
Figure 4
Figure 4
Outpatient COVID-19 cohort entry over calendar time.
Figure 5
Figure 5
COVID-19 vaccination cohort entry over calendar time.
See this image and copyright information in PMC

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