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Making Study Populations Visible Through Knowledge Graphs

  • Shruthi ChariEmail author
  • Miao Qi
  • Nkechinyere N. Agu
  • Oshani Seneviratne
  • James P. McCusker
  • Kristin P. Bennett
  • Amar K. Das
  • Deborah L. McGuinness
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11779)

Abstract

Treatment recommendations within Clinical Practice Guidelines (CPGs) are largely based on findings from clinical trials and case studies, referred to here as research studies, that are often based on highly selective clinical populations, referred to here as study cohorts. When medical practitioners apply CPG recommendations, they need to understand how well their patient population matches the characteristics of those in the study cohort, and thus are confronted with the challenges of locating the study cohort information and making an analytic comparison. To address these challenges, we develop an ontology-enabled prototype system, which exposes the population descriptions in research studies in a declarative manner, with the ultimate goal of allowing medical practitioners to better understand the applicability and generalizability of treatment recommendations. We build a Study Cohort Ontology (SCO) to encode the vocabulary of study population descriptions, that are often reported in the first table in the published work, thus they are often referred to as Table 1. We leverage the well-used Semanticscience Integrated Ontology (SIO) for defining property associations between classes. Further, we model the key components of Table 1s, i.e., collections of study subjects, subject characteristics, and statistical measures in RDF knowledge graphs. We design scenarios for medical practitioners to perform population analysis, and generate cohort similarity visualizations to determine the applicability of a study population to the clinical population of interest. Our semantic approach to make study populations visible, by standardized representations of Table 1s, allows users to quickly derive clinically relevant inferences about study populations.

Resource Website: https://tetherless-world.github.io/study-cohort-ontology/.

Keywords

Scientific Study Data Analysis Knowledge graphs Modeling Aggregations and Summary Statistics Ontology Development 

Notes

Acknowledgements

This work is partially supported by IBM Research AI through the AI Horizons Network. We thank our colleagues from IBM Research, Dan Gruen, Morgan Foreman and Ching-Hua Chen, and from RPI, John Erickson, Alexander New, and Rebecca Cowan, who greatly assisted the research.

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Rensselaer Polytechnic InstituteTroyUSA
  2. 2.IBM ResearchCambridgeUSA

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