SNOMED CT standard ontology based on the ontology for general medical science

Shaker El-Sappagh,Kyung-Sup Kwak,Farman Ali,Francesco Franda

doi:10.1186/s12911-018-0651-5

Abstract

BackgroundSystematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is a comprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic health data. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but these efforts have been hampered by the size and complexity of SCT.MethodOur proposal here is to develop an upper-level ontology and to use it as the basis for defining the terms in SCT in a way that will support quality assurance of SCT, for example, by allowing consistency checks of definitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-level SCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS).ResultsThe SCTO is implemented in OWL 2, to support automatic inference and consistency checking. The approach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundry ontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-level ontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555 annotations. It is publicly available through the bioportal at http://bioportal.bioontology.org/ontologies/SCTO/.ConclusionThe resulting ontology can enhance the semantics of clinical decision support systems and semantic interoperability among distributed electronic health records. In addition, the populated ontology can be used for the automation of mobile health applications.

Highlights

Systematized Nomenclature of Medicine—Clinical Terms (SNOMED Systematized nomenclature of medicine—clinical terms (CT), hereafter abbreviated SNOMED CT (SCT)) is a comprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic health data
The SCT ontology (SCTO) is implemented in Web ontology language (OWL) 2, to support automatic inference and consistency checking
The goal of standardized clinical terminology such as Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is to create a taxonomy of terms referring to entities in a given medical environment [2,3,4,5,6,7,8] and a framework of rules guaranteeing that each term is used with exactly one meaning; each meaning salient in the environment is expressed using exactly one term [9]

Summary

Introduction

Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is a comprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic health data. The goal of standardized clinical terminology such as Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is to create a taxonomy of terms referring to entities in a given medical environment [2,3,4,5,6,7,8] and a framework of rules guaranteeing that each term is used with exactly one meaning; each meaning salient in the environment is expressed using exactly one term [9]. There have been significant developments in both logic-based formalisms and ontology design since

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