Auditing SNOMED CT hierarchical relations based on lexical features of concepts in non-lattice subgraphs

J Biomed Inform. 2018 Feb;78:177-184. doi: 10.1016/j.jbi.2017.12.010. Epub 2017 Dec 20.

Abstract

Objective: We introduce a structural-lexical approach for auditing SNOMED CT using a combination of non-lattice subgraphs of the underlying hierarchical relations and enriched lexical attributes of fully specified concept names. Our goal is to develop a scalable and effective approach that automatically identifies missing hierarchical IS-A relations.

Methods: Our approach involves 3 stages. In stage 1, all non-lattice subgraphs of SNOMED CT's IS-A hierarchical relations are extracted. In stage 2, lexical attributes of fully-specified concept names in such non-lattice subgraphs are extracted. For each concept in a non-lattice subgraph, we enrich its set of attributes with attributes from its ancestor concepts within the non-lattice subgraph. In stage 3, subset inclusion relations between the lexical attribute sets of each pair of concepts in each non-lattice subgraph are compared to existing IS-A relations in SNOMED CT. For concept pairs within each non-lattice subgraph, if a subset relation is identified but an IS-A relation is not present in SNOMED CT IS-A transitive closure, then a missing IS-A relation is reported. The September 2017 release of SNOMED CT (US edition) was used in this investigation.

Results: A total of 14,380 non-lattice subgraphs were extracted, from which we suggested a total of 41,357 missing IS-A relations. For evaluation purposes, 200 non-lattice subgraphs were randomly selected from 996 smaller subgraphs (of size 4, 5, or 6) within the "Clinical Finding" and "Procedure" sub-hierarchies. Two domain experts confirmed 185 (among 223) suggested missing IS-A relations, a precision of 82.96%.

Conclusions: Our results demonstrate that analyzing the lexical features of concepts in non-lattice subgraphs is an effective approach for auditing SNOMED CT.

Keywords: Biomedical ontologies; Lexical attributes; Non-lattice subgraphs; Quality assurance; SNOMED CT.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Biological Ontologies*
  • Data Mining / methods*
  • Electronic Health Records
  • Humans
  • Medical Audit
  • Quality Assurance, Health Care / standards*
  • Semantics
  • Systematized Nomenclature of Medicine*