Clinical Epidemiology (Sep 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

  • Raventós B,
  • Fernández-Bertolín S,
  • Aragón M,
  • Voss EA,
  • Blacketer C,
  • Méndez-Boo L,
  • Recalde M,
  • Roel E,
  • Pistillo A,
  • Reyes C,
  • van Sandijk S,
  • Halvorsen L,
  • Rijnbeek PR,
  • Burn E,
  • Duarte-Salles T

Journal volume & issue
Vol. Volume 15
pp. 969 – 986

Abstract

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Berta Raventós,1,2,* Sergio Fernández-Bertolín,1,* María Aragón,1 Erica A Voss,3– 5 Clair Blacketer,3– 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-Salles1,4 1Fundació Institut Universitari per a la recerca a l’Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain; 2Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain; 3Janssen Pharmaceutical Research and Development, Titusville, NJ, USA; 4Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, the Netherlands; 5OHDSI Collaborators, Observational Health Data Sciences and Informatics (OHDSI), New York, NY, USA; 6Sistemes d’Informació dels Serveis d’Atenció Primària (SISAP), Institut Català de la Salut, Barcelona, Spain; 7Universitat Pompeu Fabra, Barcelona, Spain; 8Odysseus Data Services s.r.o., Prague, Czech Republic; 9edenceHealth NV, Kontich, Belgium; 10Centre for Statistics in Medicine, University of Oxford, Oxford, UK*These authors contributed equally to this workCorrespondence: Talita Duarte-Salles, Fundació Institut Universitari per a la recerca a l’Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Gran Via Corts Catalanes, 587 àtic, Barcelona, 08007, Spain, Tel +34935824342, Email [email protected]: 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: electronic health records, medical ontologies, secondary data use, common data model, OMOP

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