Cohort Identification Using Semantic Web Technologies: Triplestores as Engines for Complex Computable Phenotyping

BackgroundComputable phenotypes are increasingly important tools for patient cohort identification. As part of a study of risk of chronic opioid use after surgery, we used a Resource Description Framework (RDF) triplestore as our computable phenotyping platform, hypothesizing that the unique affordances of triplestores may aid in making complex computable phenotypes more interoperable and reproducible than traditional relational database queries. To identify and model risk for new chronic opioid users post-surgery, we loaded several heterogeneous data sources into a Blazegraph triplestore: (1) electronic health record data; (2) claims data; (3) American Community Survey data; and (4) Centers for Disease Control Social Vulnerability Index, opioid prescription rate, and drug poisoning rate data. We then ran a series of queries to execute each of the rules in our "new chronic opioid user" phenotype definition to ultimately arrive at our qualifying cohort. ResultsOf the 4,163 patients in the denominator, our computable phenotype identified 248 patients as new chronic opioid users after their index surgical procedure. After validation against charts, 228 of the 248 were revealed to be true positive cases, giving our phenotype a PPV of 0.92. ConclusionWe successfully used the triplestore to execute the new chronic opioid user phenotype logic, and in doing so noted some advantages of the triplestore in terms of schemalessness, interoperability, and reproducibility. Future work will use the triplestore to create the planned risk model and leverage the additional links with ontologies, and ontological reasoning.