Toward cross-platform electronic health record-driven phenotyping using Clinical Quality Language. Academic Article uri icon



  • Introduction: Electronic health record (EHR)-driven phenotyping is a critical first step in generating biomedical knowledge from EHR data. Despite recent progress, current phenotyping approaches are manual, time-consuming, error-prone, and platform-specific. This results in duplication of effort and highly variable results across systems and institutions, and is not scalable or portable. In this work, we investigate how the nascent Clinical Quality Language (CQL) can address these issues and enable high-throughput, cross-platform phenotyping. Methods: We selected a clinically validated heart failure (HF) phenotype definition and translated it into CQL, then developed a CQL execution engine to integrate with the Observational Health Data Sciences and Informatics (OHDSI) platform. We executed the phenotype definition at two large academic medical centers, Northwestern Medicine and Weill Cornell Medicine, and conducted results verification (n = 100) to determine precision and recall. We additionally executed the same phenotype definition against two different data platforms, OHDSI and Fast Healthcare Interoperability Resources (FHIR), using the same underlying dataset and compared the results. Results: CQL is expressive enough to represent the HF phenotype definition, including Boolean and aggregate operators, and temporal relationships between data elements. The language design also enabled the implementation of a custom execution engine with relative ease, and results verification at both sites revealed that precision and recall were both 100%. Cross-platform execution resulted in identical patient cohorts generated by both data platforms. Conclusions: CQL supports the representation of arbitrarily complex phenotype definitions, and our execution engine implementation demonstrated cross-platform execution against two widely used clinical data platforms. The language thus has the potential to help address current limitations with portability in EHR-driven phenotyping and scale in learning health systems.

publication date

  • June 25, 2020


PubMed Central ID

  • PMC7556419

Scopus Document Identifier

  • 85087153567

Digital Object Identifier (DOI)

  • 10.1002/lrh2.10233

PubMed ID

  • 33083538

Additional Document Info


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