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PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability.

Jacqueline C Kirby1, Peter Speltz1, Luke V Rasmussen2

  • 1Vanderbilt University Medical Center, Nashville, TN, USA.

Journal of the American Medical Informatics Association : JAMIA
|March 31, 2016
PubMed
Summary

Phenotype KnowledgeBase (PheKB) facilitates the creation and sharing of electronic health record (EHR) phenotype algorithms. These algorithms demonstrate high performance and transportability across healthcare systems for clinical research.

Keywords:
clinical researchelectronic health recordselectronic phenotypinggenomic researchnatural language processing

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Area of Science:

  • Biomedical Informatics
  • Health Data Science
  • Clinical Research Informatics

Background:

  • Electronic health records (EHRs) are crucial for clinical and genomic research.
  • Developing accurate phenotype algorithms is essential for identifying patient cohorts.
  • Sharing and validating these algorithms across institutions enhances their utility.

Purpose of the Study:

  • To report the status and impact of the Phenotype KnowledgeBase (PheKB).
  • To analyze components and performance of electronic phenotype algorithms.
  • To assess the transportability of algorithms between healthcare systems.

Main Methods:

  • Utilized PheKB, an online platform for building, sharing, and validating phenotype algorithms.
  • Analyzed algorithm components (e.g., ICD codes, medications, NLP) and their usage.
  • Evaluated algorithm performance at authoring and secondary implementation sites.

Main Results:

  • PheKB hosts 30 finalized and 62 developing phenotype algorithms.
  • Algorithms have high view counts and inter-institutional reuse.
  • Median positive predictive values (PPVs) for algorithms were high and consistent across sites (Case: ~96-97.5%, Control: 100%).

Conclusions:

  • Electronic phenotype algorithms can be developed with high PPV using EHR data.
  • Algorithms developed at one institution are generally transportable to others.
  • PheKB supports the development, transportability, and validity of research-grade phenotypes.