ArticleJournal of biomedical informatics2022
FHIR-Ontop-OMOP: Building clinical knowledge graphs in FHIR RDF with the OMOP Common data Model.
Article in Journal of biomedical informatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Common data models and data standards for tabular health data: a systematic review.BMC medical informatics and decision making · 2025Pooled it
- Advancing real-world evidence in Brazil: regulatory gaps and global lessons.Lancet regional health. Americas · 2026Review
- Digital-Intelligent Precision Health Management: An Integrative Framework for Chronic Disease Prevention and Control.Biomedicines · 2026Article
- Research on the construction and application of pathology knowledge graph.BMC medical education · 2025Article
- Hospital-wide, dynamic, individualized prediction of central line-associated bloodstream infections-development and temporal evaluation of six prediction models.BMC infectious diseases · 2025Article
- Interoperability Framework of the European Health Data Space for the Secondary Use of Data: Interactive European Interoperability Framework-Based Standards Compliance Toolkit for AI-Driven Projects.Journal of medical Internet research · 2025Article
- An ontology-based rare disease common data model harmonising international registries, FHIR, and Phenopackets.Scientific data · 2025Article
- Cross-Standard Health Data Harmonization using Semantics of Data Elements.Scientific data · 2024Article
- State-of-the-Art Fast Healthcare Interoperability Resources (FHIR)-Based Data Model and Structure Implementations: Systematic Scoping Review.JMIR medical informatics · 2024Article
- Electronic Health Record-Oriented Knowledge Graph System for Collaborative Clinical Decision Support Using Multicenter Fragmented Medical Data: Design and Application Study.Journal of medical Internet research · 2024Article
- MENDS-on-FHIR: leveraging the OMOP common data model and FHIR standards for national chronic disease surveillance.JAMIA open · 2024Article
- A Novel Sentence Transformer-based Natural Language Processing Approach for Schema Mapping of Electronic Health Records to the OMOP Common Data Model.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2024Article
- MENDS-on-FHIR: Leveraging the OMOP common data model and FHIR standards for national chronic disease surveillance.medRxiv : the preprint server for health sciences · 2023Article
- Machine Learning-Enabled Clinical Information Systems Using Fast Healthcare Interoperability Resources Data Standards: Scoping Review.JMIR medical informatics · 2023Article
- Capturing Semantic Relationships in Electronic Health Records Using Knowledge Graphs: An Implementation Using MIMIC III Dataset and GraphDB.Healthcare (Basel, Switzerland) · 2023Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
backgroundKnowledge graphs (KGs) play a key role to enable explainable artificial intelligence (AI) applications in healthcare. Constructing clinical knowledge graphs (CKGs) against heterogeneous electronic health records (EHRs) has been desired by the research and healthcare AI communities. From the standardization perspective, community-based standards such as the Fast Healthcare Interoperability Resources (FHIR) and the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) are increasingly used to represent and standardize EHR data for clinical data analytics, however, the potential of such a standard on building CKG has not been well investigated.
objectiveTo develop and evaluate methods and tools that expose the OMOP CDM-based clinical data repositories into virtual clinical KGs that are compliant with FHIR Resource Description Framework (RDF) specification.
methodsWe developed a system called FHIR-Ontop-OMOP to generate virtual clinical KGs from the OMOP relational databases. We leveraged an OMOP CDM-based Medical Information Mart for Intensive Care (MIMIC-III) data repository to evaluate the FHIR-Ontop-OMOP system in terms of the faithfulness of data transformation and the conformance of the generated CKGs to the FHIR RDF specification.
resultsA beta version of the system has been released. A total of more than 100 data element mappings from 11 OMOP CDM clinical data, health system and vocabulary tables were implemented in the system, covering 11 FHIR resources. The generated virtual CKG from MIMIC-III contains 46,520 instances of FHIR Patient, 716,595 instances of Condition, 1,063,525 instances of Procedure, 24,934,751 instances of MedicationStatement, 365,181,104 instances of Observations, and 4,779,672 instances of CodeableConcept. Patient counts identified by five pairs of SQL (over the MIMIC database) and SPARQL (over the virtual CKG) queries were identical, ensuring the faithfulness of the data transformation. Generated CKG in RDF triples for 100 patients were fully conformant with the FHIR RDF specification.
conclusionThe FHIR-Ontop-OMOP system can expose OMOP database as a FHIR-compliant RDF graph. It provides a meaningful use case demonstrating the potentials that can be enabled by the interoperability between FHIR and OMOP CDM. Generated clinical KGs in FHIR RDF provide a semantic foundation to enable explainable AI applications in healthcare.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.