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Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties

Background: Formal definitions allow selecting terms (e.g., identifying all terms related to “Infectious disease” using the query “has causative agent organism”) and terminological reasoning (e.g., “hepatitis B” is a “hepatitis” and is an “infectious disease”). However, the standard international te...

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Autores principales: Bousquet, Cédric, Souvignet, Julien, Sadou, Éric, Jaulent, Marie-Christine, Declerck, Gunnar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6747929/
https://www.ncbi.nlm.nih.gov/pubmed/31551780
http://dx.doi.org/10.3389/fphar.2019.00975
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author Bousquet, Cédric
Souvignet, Julien
Sadou, Éric
Jaulent, Marie-Christine
Declerck, Gunnar
author_facet Bousquet, Cédric
Souvignet, Julien
Sadou, Éric
Jaulent, Marie-Christine
Declerck, Gunnar
author_sort Bousquet, Cédric
collection PubMed
description Background: Formal definitions allow selecting terms (e.g., identifying all terms related to “Infectious disease” using the query “has causative agent organism”) and terminological reasoning (e.g., “hepatitis B” is a “hepatitis” and is an “infectious disease”). However, the standard international terminology Medical Dictionary for Regulatory Activities (MedDRA) used for coding adverse drug reactions in pharmacovigilance databases does not beneficiate from such formal definitions. Our objective was to evaluate the potential of reuse of ontological and non-ontological resources for generating such definitions for MedDRA. Methods: We developed several methods that collectively allow a semiautomatic semantic enrichment of MedDRA: 1) using MedDRA-to-SNOMED Clinical Terms (SNOMED CT) mappings (available in the Unified Medical Language System metathesaurus or other mapping resources, e.g., the MedDRA preferred term “hepatitis B” is associated to the SNOMED CT concept “type B viral hepatitis”) to extract term definitions (e.g., “hepatitis B” is associated with the following properties: has finding site liver structure, has associated morphology inflammation morphology, and has causative agent hepatitis B virus); 2) using MedDRA labels and lexical/syntactic methods for automatic decomposition of complex MedDRA terms (e.g., the MedDRA systems organ class “blood and lymphatic system disorders” is decomposed in blood system disorders and lymphatic system disorders) or automatic suggestions of properties (e.g., the string “cyclic” in preferred term “cyclic neutropenia” leads to the property has clinical course cyclic). Results: The Unified Medical Language System metathesaurus was the main ontological resource reusable for generating formal definitions for MedDRA terms. The non-ontological resources (another mapping resource provided by Nadkarni and Darer in 2010 and MedDRA labels) allowed defining few additional preferred terms. While the Ci4SeR tool helped the curator to define 1,935 terms by suggesting potential supplemental relations based on the parents’ and siblings’ semantic definition, defining manually all MedDRA terms remains expensive in time. Discussion: Several ontological and non-ontological resources are available for associating MedDRA terms to SNOMED CT concepts with semantic properties, but providing manual definitions is still necessary. The ontology of adverse events is a possible alternative but does not cover all MedDRA terms either. Perspectives are to implement more efficient techniques to find more logical relations between SNOMED CT and MedDRA in an automated way.
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spelling pubmed-67479292019-09-24 Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties Bousquet, Cédric Souvignet, Julien Sadou, Éric Jaulent, Marie-Christine Declerck, Gunnar Front Pharmacol Pharmacology Background: Formal definitions allow selecting terms (e.g., identifying all terms related to “Infectious disease” using the query “has causative agent organism”) and terminological reasoning (e.g., “hepatitis B” is a “hepatitis” and is an “infectious disease”). However, the standard international terminology Medical Dictionary for Regulatory Activities (MedDRA) used for coding adverse drug reactions in pharmacovigilance databases does not beneficiate from such formal definitions. Our objective was to evaluate the potential of reuse of ontological and non-ontological resources for generating such definitions for MedDRA. Methods: We developed several methods that collectively allow a semiautomatic semantic enrichment of MedDRA: 1) using MedDRA-to-SNOMED Clinical Terms (SNOMED CT) mappings (available in the Unified Medical Language System metathesaurus or other mapping resources, e.g., the MedDRA preferred term “hepatitis B” is associated to the SNOMED CT concept “type B viral hepatitis”) to extract term definitions (e.g., “hepatitis B” is associated with the following properties: has finding site liver structure, has associated morphology inflammation morphology, and has causative agent hepatitis B virus); 2) using MedDRA labels and lexical/syntactic methods for automatic decomposition of complex MedDRA terms (e.g., the MedDRA systems organ class “blood and lymphatic system disorders” is decomposed in blood system disorders and lymphatic system disorders) or automatic suggestions of properties (e.g., the string “cyclic” in preferred term “cyclic neutropenia” leads to the property has clinical course cyclic). Results: The Unified Medical Language System metathesaurus was the main ontological resource reusable for generating formal definitions for MedDRA terms. The non-ontological resources (another mapping resource provided by Nadkarni and Darer in 2010 and MedDRA labels) allowed defining few additional preferred terms. While the Ci4SeR tool helped the curator to define 1,935 terms by suggesting potential supplemental relations based on the parents’ and siblings’ semantic definition, defining manually all MedDRA terms remains expensive in time. Discussion: Several ontological and non-ontological resources are available for associating MedDRA terms to SNOMED CT concepts with semantic properties, but providing manual definitions is still necessary. The ontology of adverse events is a possible alternative but does not cover all MedDRA terms either. Perspectives are to implement more efficient techniques to find more logical relations between SNOMED CT and MedDRA in an automated way. Frontiers Media S.A. 2019-09-10 /pmc/articles/PMC6747929/ /pubmed/31551780 http://dx.doi.org/10.3389/fphar.2019.00975 Text en Copyright © 2019 Bousquet, Souvignet, Sadou, Jaulent and Declerck http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Pharmacology
Bousquet, Cédric
Souvignet, Julien
Sadou, Éric
Jaulent, Marie-Christine
Declerck, Gunnar
Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties
title Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties
title_full Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties
title_fullStr Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties
title_full_unstemmed Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties
title_short Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties
title_sort ontological and non-ontological resources for associating medical dictionary for regulatory activities terms to snomed clinical terms with semantic properties
topic Pharmacology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6747929/
https://www.ncbi.nlm.nih.gov/pubmed/31551780
http://dx.doi.org/10.3389/fphar.2019.00975
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