Clinical MetaData ontology: a simple classification scheme for data elements of clinical data based on semantics
Abstract Background The increasing use of common data elements (CDEs) in numerous research projects and clinical applications has made it imperative to create an effective classification scheme for the efficient management of these data elements. We applied high-level integrative modeling of entire...
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doaj-38dd27bd3fc14b20b2621f2d956947692020-11-25T03:54:35ZengBMCBMC Medical Informatics and Decision Making1472-69472019-08-0119111110.1186/s12911-019-0877-xClinical MetaData ontology: a simple classification scheme for data elements of clinical data based on semanticsHye Hyeon Kim0Yu Rang Park1Kye Hwa Lee2Young Soo Song3Ju Han Kim4Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of MedicineDepartment of Biomedical Systems Informatics, Yonsei University College of MedicinePrecision Medicine Center, Seoul National University HospitalDepartment of Pathology, Hanyang University College of MedicineSeoul National University Biomedical Informatics (SNUBI), Seoul National University College of MedicineAbstract Background The increasing use of common data elements (CDEs) in numerous research projects and clinical applications has made it imperative to create an effective classification scheme for the efficient management of these data elements. We applied high-level integrative modeling of entire clinical documents from real-world practice to create the Clinical MetaData Ontology (CMDO) for the appropriate classification and integration of CDEs that are in practical use in current clinical documents. Methods CMDO was developed using the General Formal Ontology method with a manual iterative process comprising five steps: (1) defining the scope of CMDO by conceptualizing its first-level terms based on an analysis of clinical-practice procedures, (2) identifying CMDO concepts for representing clinical data of general CDEs by examining how and what clinical data are generated with flows of clinical care practices, (3) assigning hierarchical relationships for CMDO concepts, (4) developing CMDO properties (e.g., synonyms, preferred terms, and definitions) for each CMDO concept, and (5) evaluating the utility of CMDO. Results We created CMDO comprising 189 concepts under the 4 first-level classes of Description, Event, Finding, and Procedure. CMDO has 256 definitions that cover the 189 CMDO concepts, with 459 synonyms for 139 (74.0%) of the concepts. All of the CDEs extracted from 6 HL7 templates, 25 clinical documents of 5 teaching hospitals, and 1 personal health record specification were successfully annotated by 41 (21.9%), 89 (47.6%), and 13 (7.0%) of the CMDO concepts, respectively. We created a CMDO Browser to facilitate navigation of the CMDO concept hierarchy and a CMDO-enabled CDE Browser for displaying the relationships between CMDO concepts and the CDEs extracted from the clinical documents that are used in current practice. Conclusions CMDO is an ontology and classification scheme for CDEs used in clinical documents. Given the increasing use of CDEs in many studies and real-world clinical documentation, CMDO will be a useful tool for integrating numerous CDEs from different research projects and clinical documents. The CMDO Browser and CMDO-enabled CDE Browser make it easy to search, share, and reuse CDEs, and also effectively integrate and manage CDEs from different studies and clinical documents.http://link.springer.com/article/10.1186/s12911-019-0877-xOntologyCommon data elementISO/IEC 11179Classification |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hye Hyeon Kim Yu Rang Park Kye Hwa Lee Young Soo Song Ju Han Kim |
spellingShingle |
Hye Hyeon Kim Yu Rang Park Kye Hwa Lee Young Soo Song Ju Han Kim Clinical MetaData ontology: a simple classification scheme for data elements of clinical data based on semantics BMC Medical Informatics and Decision Making Ontology Common data element ISO/IEC 11179 Classification |
author_facet |
Hye Hyeon Kim Yu Rang Park Kye Hwa Lee Young Soo Song Ju Han Kim |
author_sort |
Hye Hyeon Kim |
title |
Clinical MetaData ontology: a simple classification scheme for data elements of clinical data based on semantics |
title_short |
Clinical MetaData ontology: a simple classification scheme for data elements of clinical data based on semantics |
title_full |
Clinical MetaData ontology: a simple classification scheme for data elements of clinical data based on semantics |
title_fullStr |
Clinical MetaData ontology: a simple classification scheme for data elements of clinical data based on semantics |
title_full_unstemmed |
Clinical MetaData ontology: a simple classification scheme for data elements of clinical data based on semantics |
title_sort |
clinical metadata ontology: a simple classification scheme for data elements of clinical data based on semantics |
publisher |
BMC |
series |
BMC Medical Informatics and Decision Making |
issn |
1472-6947 |
publishDate |
2019-08-01 |
description |
Abstract Background The increasing use of common data elements (CDEs) in numerous research projects and clinical applications has made it imperative to create an effective classification scheme for the efficient management of these data elements. We applied high-level integrative modeling of entire clinical documents from real-world practice to create the Clinical MetaData Ontology (CMDO) for the appropriate classification and integration of CDEs that are in practical use in current clinical documents. Methods CMDO was developed using the General Formal Ontology method with a manual iterative process comprising five steps: (1) defining the scope of CMDO by conceptualizing its first-level terms based on an analysis of clinical-practice procedures, (2) identifying CMDO concepts for representing clinical data of general CDEs by examining how and what clinical data are generated with flows of clinical care practices, (3) assigning hierarchical relationships for CMDO concepts, (4) developing CMDO properties (e.g., synonyms, preferred terms, and definitions) for each CMDO concept, and (5) evaluating the utility of CMDO. Results We created CMDO comprising 189 concepts under the 4 first-level classes of Description, Event, Finding, and Procedure. CMDO has 256 definitions that cover the 189 CMDO concepts, with 459 synonyms for 139 (74.0%) of the concepts. All of the CDEs extracted from 6 HL7 templates, 25 clinical documents of 5 teaching hospitals, and 1 personal health record specification were successfully annotated by 41 (21.9%), 89 (47.6%), and 13 (7.0%) of the CMDO concepts, respectively. We created a CMDO Browser to facilitate navigation of the CMDO concept hierarchy and a CMDO-enabled CDE Browser for displaying the relationships between CMDO concepts and the CDEs extracted from the clinical documents that are used in current practice. Conclusions CMDO is an ontology and classification scheme for CDEs used in clinical documents. Given the increasing use of CDEs in many studies and real-world clinical documentation, CMDO will be a useful tool for integrating numerous CDEs from different research projects and clinical documents. The CMDO Browser and CMDO-enabled CDE Browser make it easy to search, share, and reuse CDEs, and also effectively integrate and manage CDEs from different studies and clinical documents. |
topic |
Ontology Common data element ISO/IEC 11179 Classification |
url |
http://link.springer.com/article/10.1186/s12911-019-0877-x |
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