PMID- 36884279 OWN - NLM STAT- PubMed-not-MEDLINE LR - 20230328 IS - 2291-9694 (Print) IS - 2291-9694 (Electronic) VI - 11 DP - 2023 Mar 8 TI - An Ontology-Based Approach for Consolidating Patient Data Standardized With European Norm/International Organization for Standardization 13606 (EN/ISO 13606) Into Joint Observational Medical Outcomes Partnership (OMOP) Repositories: Description of a Methodology. PG - e44547 LID - 10.2196/44547 [doi] LID - e44547 AB - BACKGROUND: To discover new knowledge from data, they must be correct and in a consistent format. OntoCR, a clinical repository developed at Hospital Clinic de Barcelona, uses ontologies to represent clinical knowledge and map locally defined variables to health information standards and common data models. OBJECTIVE: The aim of the study is to design and implement a scalable methodology based on the dual-model paradigm and the use of ontologies to consolidate clinical data from different organizations in a standardized repository for research purposes without loss of meaning. METHODS: First, the relevant clinical variables are defined, and the corresponding European Norm/International Organization for Standardization (EN/ISO) 13606 archetypes are created. Data sources are then identified, and an extract, transform, and load process is carried out. Once the final data set is obtained, the data are transformed to create EN/ISO 13606-normalized electronic health record (EHR) extracts. Afterward, ontologies that represent archetyped concepts and map them to EN/ISO 13606 and Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) standards are created and uploaded to OntoCR. Data stored in the extracts are inserted into its corresponding place in the ontology, thus obtaining instantiated patient data in the ontology-based repository. Finally, data can be extracted via SPARQL queries as OMOP CDM-compliant tables. RESULTS: Using this methodology, EN/ISO 13606-standardized archetypes that allow for the reuse of clinical information were created, and the knowledge representation of our clinical repository by modeling and mapping ontologies was extended. Furthermore, EN/ISO 13606-compliant EHR extracts of patients (6803), episodes (13,938), diagnosis (190,878), administered medication (222,225), cumulative drug dose (222,225), prescribed medication (351,247), movements between units (47,817), clinical observations (6,736,745), laboratory observations (3,392,873), limitation of life-sustaining treatment (1,298), and procedures (19,861) were created. Since the creation of the application that inserts data from extracts into the ontologies is not yet finished, the queries were tested and the methodology was validated by importing data from a random subset of patients into the ontologies using a locally developed Protege plugin ("OntoLoad"). In total, 10 OMOP CDM-compliant tables ("Condition_occurrence," 864 records; "Death," 110; "Device_exposure," 56; "Drug_exposure," 5609; "Measurement," 2091; "Observation," 195; "Observation_period," 897; "Person," 922; "Visit_detail," 772; and "Visit_occurrence," 971) were successfully created and populated. CONCLUSIONS: This study proposes a methodology for standardizing clinical data, thus allowing its reuse without any changes in the meaning of the modeled concepts. Although this paper focuses on health research, our methodology suggests that the data be initially standardized per EN/ISO 13606 to obtain EHR extracts with a high level of granularity that can be used for any purpose. Ontologies constitute a valuable approach for knowledge representation and standardization of health information in a standard-agnostic manner. With the proposed methodology, institutions can go from local raw data to standardized, semantically interoperable EN/ISO 13606 and OMOP repositories. CI - (c)Santiago Frid, Xavier Pastor Duran, Guillem Bracons Cuco, Miguel Pedrera-Jimenez, Pablo Serrano-Balazote, Adolfo Munoz Carrero, Raimundo Lozano-Rubi. Originally published in JMIR Medical Informatics (https://medinform.jmir.org), 08.03.2023. FAU - Frid, Santiago AU - Frid S AUID- ORCID: 0000-0001-8400-5770 AD - Medical Informatics Unit, Hospital Clinic de Barcelona, Barcelona, Spain. AD - Clinical Foundations Department, Universitat de Barcelona, Barcelona, Spain. FAU - Pastor Duran, Xavier AU - Pastor Duran X AUID- ORCID: 0000-0001-8267-7151 AD - Medical Informatics Unit, Hospital Clinic de Barcelona, Barcelona, Spain. AD - Clinical Foundations Department, Universitat de Barcelona, Barcelona, Spain. FAU - Bracons Cuco, Guillem AU - Bracons Cuco G AUID- ORCID: 0000-0003-1274-7403 AD - Fundacio Clinic per a la Recerca Biomedica, Barcelona, Spain. FAU - Pedrera-Jimenez, Miguel AU - Pedrera-Jimenez M AUID- ORCID: 0000-0003-0187-3826 AD - Data Science Unit, Hospital 12 de Octubre, Madrid, Spain. FAU - Serrano-Balazote, Pablo AU - Serrano-Balazote P AUID- ORCID: 0000-0003-2958-6319 AD - Direction of Planification, Hospital 12 de Octubre, Madrid, Spain. FAU - Munoz Carrero, Adolfo AU - Munoz Carrero A AUID- ORCID: 0000-0002-0141-7751 AD - Unit of Investigation in Telemedicine and Digital Health, Instituto de Salud Carlos III, Madrid, Spain. FAU - Lozano-Rubi, Raimundo AU - Lozano-Rubi R AUID- ORCID: 0000-0002-7912-721X AD - Medical Informatics Unit, Hospital Clinic de Barcelona, Barcelona, Spain. AD - Clinical Foundations Department, Universitat de Barcelona, Barcelona, Spain. LA - eng PT - Journal Article DEP - 20230308 PL - Canada TA - JMIR Med Inform JT - JMIR medical informatics JID - 101645109 PMC - PMC10034609 OTO - NOTNLM OT - European Norm/International Organization for Standardization 13606 OT - Observational Medical Outcomes Partnership Common Data Model OT - clinical data OT - dual model OT - health information interoperability OT - health information standards OT - health records OT - health research OT - ontologies OT - secondary use of health data COIS- Conflicts of Interest: None declared. EDAT- 2023/03/09 06:00 MHDA- 2023/03/09 06:01 PMCR- 2023/03/08 CRDT- 2023/03/08 11:53 PHST- 2022/11/23 00:00 [received] PHST- 2023/01/05 00:00 [accepted] PHST- 2022/12/28 00:00 [revised] PHST- 2023/03/08 11:53 [entrez] PHST- 2023/03/09 06:00 [pubmed] PHST- 2023/03/09 06:01 [medline] PHST- 2023/03/08 00:00 [pmc-release] AID - v11i1e44547 [pii] AID - 10.2196/44547 [doi] PST - epublish SO - JMIR Med Inform. 2023 Mar 8;11:e44547. doi: 10.2196/44547.