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

Abstract

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.

The role of COVID-19 vaccines in preventing post-COVID-19 thromboembolic and cardiovascular complications

“… 14 CPRD Aurum currently covers 13 million people from predominantly English practices, while CPRD Gold comprises 3.1 million active participants mostly from GP practices in Wales and Scotland. Spanish data were provided by the Information System for the Development of Research in Primary Care (SIDIAP), 15 which encompasses primary care records from 6 million active patients (around 75% of the population in the region of Catalonia) linked to hospital admissions data (Conjunt Mínim Bàsic de Dades d’Alta Hospitalària). Finally, the CORIVA dataset based on national health claims data from Estonia was used.…”

IncidencePrevalence: An R package to calculate population‐level incidence rates and prevalence using the OMOP common data model

“…17 IncidencePrevalence is designed to be used against data mapped to the OMOP CDM, and therefore, data sets must be first converted to the CDM prior to using the package presented in this paper. [18][19][20] Inci-dencePrevalence can connect to several database management systems through the DataBase Interface (DBI) R package. 21 To allow for a pipe friendly syntax, CDM table references are stored in a single object (referred as cdm object) through the CDMConnector R package.…”

Socioeconomic inequalities in COVID-19 infection and vaccine uptake among children and adolescents in Catalonia, Spain

“…SIDIAP includes information on sociodemographics, disease diagnoses, laboratory tests, medication use and death 12 . In addition, this database has been linked to the Catalan public health vaccine registry and to a population-based register of hospital discharge records from public and private hospitals of Catalonia (Conjunt Mínim Bàsic de Dades d'Alta Hospitalària, CMBD-AH) 13 . It has been standardized to the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM), and the provenance of the data, specifically for capturing COVID-19-related outcomes, has been well documented 14 .…”