Knowledge Driven Phenotyping

Abstract

Extracting patient phenotypes from routinely collected health data (such as Electronic Health Records) requires translating clinically-sound phenotype definitions into queries/computations executable on the underlying data sources by clinical researchers. This requires significant knowledge and skills to deal with heterogeneous and often imperfect data. Translations are time-consuming, error-prone and, most importantly, hard to share and reproduce across different settings. This paper proposes a knowledge driven framework that (1) decouples the specification of phenotype semantics from underlying data sources; (2) can automatically populate and conduct phenotype computations on heterogeneous data spaces. We report preliminary results of deploying this framework on five Scottish health datasets.

Keywords: data integration; health data; ontology; phenotype computation.