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
Bibliographic record
Abstract
BACKGROUND: To discover new knowledge from data, they must be correct and in a consistent format. OntoCR, a clinical repository developed at Hospital Clínic 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 Protégé 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.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.020 | 0.025 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.004 |
| Bibliometrics | 0.008 | 0.007 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.008 | 0.009 |
| Open science | 0.004 | 0.008 |
| Research integrity | 0.002 | 0.003 |
| Insufficient payload (model declined to judge) | 0.003 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".