SNOMED CT Concept Hierarchies for Computable Clinical Phenotypes From Electronic Health Record Data: Comparison of Intensional Versus Extensional Value Sets (Preprint)

Abstract

Background: Defining clinical phenotypes from EHR-derived data proves crucial for clinical decision support, population health endeavors, and translational research. EHR diagnoses now commonly draw from a finely-grained clinical terminologyeither native SNOMED CT, or a vendor-supplied terminology mapped to SNOMED CT concepts as the standard for EHR interoperability. Accordingly, electronic clinical quality measures (eCQMs) increasingly define clinical phenotypes with SNOMED CT value sets. The work of creating and maintaining list-based value sets proves daunting, as does vetting that their contents accurately represent the clinicallyintended condition. Objective: To compare an intensional (concept hierarchy-based) vs. extensional (list-based) value set approach to defining clinical phenotypes using SNOMED CT encoded data from EHRs, by evaluating value set conciseness, time to create, and completeness. Methods: Starting from published CMS 2018 high-priority eCQMs, we selected ten clinical conditions referenced by those eCQMs. For each, the published SNOMED CT list-based (extensional) value set was downloaded from the Value Set Authority Center (VSAC). Ten corresponding SNOMED CT hierarchy-based intensional value sets for the same conditions were identified within our EHR. From each hierarchybased intensional value set, an exactly equivalent full extensional value set was derived enumerating all included descendant SNOMED CT concepts. Comparisons were then made between (a) (VSAC) downloaded list-based (extensional) value sets, (b) corresponding hierarchy-based intensional value sets for the same conditions, and (c) derived list-based (extensional) value sets exactly equivalent to the hierarchy-based intensional value sets. Value set conciseness was assessed by the number of SNOMED CT concepts needed for definition. Time to construct the value sets for local use was measured. Value set completeness was assessed by comparing contents of the downloaded extensional vs. intensional value sets. Two measures of content completeness were made: for individual SNOMED CT concepts, and for the mapped diagnosis clinical terms available for selection within the EHR by clinicians. Results: The 10 hierarchy-based intensional value sets proved far simpler and faster to construct than exactly equivalent derived extensional value set lists, requiring a median 3 vs. 78 concepts to define, and 5 vs. 37 min to build. The hierarchy-based intensional value sets also proved more complete: in comparison, the 10 downloaded 2018 extensional value sets contained a median of just 35% of the intensional value sets' SNOMED CT concepts and 65% of mapped EHR clinical terms. Conclusions: In the EHR era, defining conditions preferentially should employ SNOMED CT concept hierarchy-based (intensional) value sets, rather than 1 extensional lists. By doing so, clinical guideline and eCQM authors can more readily engage specialists in vetting condition subtypes to include and exclude, and streamline broad EHR implementation of condition-specific ...