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

• DOI: 10.2196/44547
• Publication Date: 2023-01-05T08:30:02Z
• Authors: Santiago Frid; Xavier Pastor Duran; Guillem Bracons Cucó; Miguel Pedrera-Ji...; Pablo Serrano-Bal...; Adolfo Muñoz Carrero; Raimundo Lozano-Rubí
• Keywords: Original Paper; Computer applications to medicine. Medical informatics; R858-859.7; 3. Good health

To discover new knowledge from data, they must be correct and in a consistent format. OntoCR, clinical repository developed at Hospital Clínic de Barcelona, uses ontologies to represent map locally defined variables health information standards common data models.The aim of the study is design implement scalable methodology based on dual-model paradigm use consolidate different organizations standardized for research purposes without loss meaning.First, relevant are defined, corresponding European Norm/International Organization Standardization (EN/ISO) 13606 archetypes created. Data sources then identified, an extract, transform, load process carried out. Once final set obtained, transformed create EN/ISO 13606-normalized electronic record (EHR) extracts. Afterward, that archetyped concepts them Observational Medical Outcomes Partnership Common Model (OMOP CDM) created uploaded OntoCR. stored extracts inserted into its place ontology, thus obtaining instantiated patient ontology-based repository. Finally, can extracted via SPARQL queries as OMOP CDM-compliant tables.Using this methodology, 13606-standardized allow reuse were created, representation our by modeling mapping was extended. Furthermore, 13606-compliant EHR patients (6803), episodes (13,938), diagnosis (190,878), administered medication (222,225), cumulative drug dose prescribed (351,247), movements between units (47,817), observations (6,736,745), laboratory (3,392,873), limitation life-sustaining treatment (1,298), procedures (19,861) Since creation application inserts not yet finished, tested validated importing random subset using Protégé plugin ("OntoLoad"). In total, 10 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; "Visit_occurrence," 971) successfully populated.This proposes standardizing allowing any changes meaning modeled concepts. Although paper focuses research, suggests initially per obtain with high level granularity used purpose. Ontologies constitute valuable approach standardization standard-agnostic manner. With proposed institutions go local raw standardized, semantically interoperable repositories.