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/.
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Notes
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Declarative manner: in a clear, unambiguous, and computer understandable manner.
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Find the list of all supported publication types at https://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.T.publication_types/.
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We use the ontology prefixes: (1) sio: SemanticScience Integrated Ontology (2) uo: The Units of Measurement Ontology (3) chear: Children’s Health Exposure Analysis Resource Ontology (4) ncit: National Cancer Institute Thesaurus (5) provcare: ProveCaRe (6) doid: Human Disease Ontology (7) sco: Study Cohort Ontology (8) hasco: Human-Aware Science Ontology (9) prov: The PROV ontology (10) dct: Dublin Core Terms (11) vann: A vocabulary for annotating vocabulary descriptions.
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View the definition of sio:hasProperty and sio:hasAttribute relations at: https://raw.githubusercontent.com/micheldumontier/semanticscience/master/ontology/sio/release/sio-subset-labels.owl.
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More Table 1 reporting style and composition details at https://prsinfo.clinicaltrials.gov/webinars/module6/resources/BaselineCharacteristics_Handouts.pdf.
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Definition adapted from: https://en.wikipedia.org/wiki/Descriptive_statistics.
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Dataset Information Page. https://wwwn.cdc.gov/nchs/nhanes/continuousnhanes/default.aspx?BeginYear=2015.
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NIH Collaboratory run grand-round presentation: https://www.nihcollaboratory.org/Pages/Grand-Rounds-02-28-14.aspx.
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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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Chari, S. et al. (2019). Making Study Populations Visible Through Knowledge Graphs. In: Ghidini, C., et al. The Semantic Web – ISWC 2019. ISWC 2019. Lecture Notes in Computer Science(), vol 11779. Springer, Cham. https://doi.org/10.1007/978-3-030-30796-7_4
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DOI: https://doi.org/10.1007/978-3-030-30796-7_4
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