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Interoperability between phenotypes in research and healthcare terminologies—Investigating partial mappings between HPO and SNOMED CT

BACKGROUND: Identifying partial mappings between two terminologies is of special importance when one terminology is finer-grained than the other, as is the case for the Human Phenotype Ontology (HPO), mainly used for research purposes, and SNOMED CT, mainly used in healthcare. OBJECTIVES: To investi...

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Autores principales: Dhombres, Ferdinand, Bodenreider, Olivier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748471/
https://www.ncbi.nlm.nih.gov/pubmed/26865946
http://dx.doi.org/10.1186/s13326-016-0047-3
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author Dhombres, Ferdinand
Bodenreider, Olivier
author_facet Dhombres, Ferdinand
Bodenreider, Olivier
author_sort Dhombres, Ferdinand
collection PubMed
description BACKGROUND: Identifying partial mappings between two terminologies is of special importance when one terminology is finer-grained than the other, as is the case for the Human Phenotype Ontology (HPO), mainly used for research purposes, and SNOMED CT, mainly used in healthcare. OBJECTIVES: To investigate and contrast lexical and logical approaches to deriving partial mappings between HPO and SNOMED CT. METHODS: 1) Lexical approach—We identify modifiers in HPO terms and attempt to map demodified terms to SNOMED CT through UMLS; 2) Logical approach—We leverage subsumption relations in HPO to infer partial mappings to SNOMED CT; 3) Comparison—We analyze the specific contribution of each approach and evaluate the quality of the partial mappings through manual review. RESULTS: There are 7358 HPO concepts with no complete mapping to SNOMED CT. We identified partial mappings lexically for 33 % of them and logically for 82 %. We identified partial mappings both lexically and logically for 27 %. The clinical relevance of the partial mappings (for a cohort selection use case) is 49 % for lexical mappings and 67 % for logical mappings. CONCLUSIONS: Through complete and partial mappings, 92 % of the 10,454 HPO concepts can be mapped to SNOMED CT (30 % complete and 62 % partial). Equivalence mappings between HPO and SNOMED CT allow for interoperability between data described using these two systems. However, due to differences in focus and granularity, equivalence is only possible for 30 % of HPO classes. In the remaining cases, partial mappings provide a next-best approach for traversing between the two systems. Both lexical and logical mapping techniques produce mappings that cannot be generated by the other technique, suggesting that the two techniques are complementary to each other. Finally, this work demonstrates interesting properties (both lexical and logical) of HPO and SNOMED CT and illustrates some limitations of mapping through UMLS.
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spelling pubmed-47484712016-02-11 Interoperability between phenotypes in research and healthcare terminologies—Investigating partial mappings between HPO and SNOMED CT Dhombres, Ferdinand Bodenreider, Olivier J Biomed Semantics Research BACKGROUND: Identifying partial mappings between two terminologies is of special importance when one terminology is finer-grained than the other, as is the case for the Human Phenotype Ontology (HPO), mainly used for research purposes, and SNOMED CT, mainly used in healthcare. OBJECTIVES: To investigate and contrast lexical and logical approaches to deriving partial mappings between HPO and SNOMED CT. METHODS: 1) Lexical approach—We identify modifiers in HPO terms and attempt to map demodified terms to SNOMED CT through UMLS; 2) Logical approach—We leverage subsumption relations in HPO to infer partial mappings to SNOMED CT; 3) Comparison—We analyze the specific contribution of each approach and evaluate the quality of the partial mappings through manual review. RESULTS: There are 7358 HPO concepts with no complete mapping to SNOMED CT. We identified partial mappings lexically for 33 % of them and logically for 82 %. We identified partial mappings both lexically and logically for 27 %. The clinical relevance of the partial mappings (for a cohort selection use case) is 49 % for lexical mappings and 67 % for logical mappings. CONCLUSIONS: Through complete and partial mappings, 92 % of the 10,454 HPO concepts can be mapped to SNOMED CT (30 % complete and 62 % partial). Equivalence mappings between HPO and SNOMED CT allow for interoperability between data described using these two systems. However, due to differences in focus and granularity, equivalence is only possible for 30 % of HPO classes. In the remaining cases, partial mappings provide a next-best approach for traversing between the two systems. Both lexical and logical mapping techniques produce mappings that cannot be generated by the other technique, suggesting that the two techniques are complementary to each other. Finally, this work demonstrates interesting properties (both lexical and logical) of HPO and SNOMED CT and illustrates some limitations of mapping through UMLS. BioMed Central 2016-02-09 /pmc/articles/PMC4748471/ /pubmed/26865946 http://dx.doi.org/10.1186/s13326-016-0047-3 Text en © Dhombres and Bodenreider. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Dhombres, Ferdinand
Bodenreider, Olivier
Interoperability between phenotypes in research and healthcare terminologies—Investigating partial mappings between HPO and SNOMED CT
title Interoperability between phenotypes in research and healthcare terminologies—Investigating partial mappings between HPO and SNOMED CT
title_full Interoperability between phenotypes in research and healthcare terminologies—Investigating partial mappings between HPO and SNOMED CT
title_fullStr Interoperability between phenotypes in research and healthcare terminologies—Investigating partial mappings between HPO and SNOMED CT
title_full_unstemmed Interoperability between phenotypes in research and healthcare terminologies—Investigating partial mappings between HPO and SNOMED CT
title_short Interoperability between phenotypes in research and healthcare terminologies—Investigating partial mappings between HPO and SNOMED CT
title_sort interoperability between phenotypes in research and healthcare terminologies—investigating partial mappings between hpo and snomed ct
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748471/
https://www.ncbi.nlm.nih.gov/pubmed/26865946
http://dx.doi.org/10.1186/s13326-016-0047-3
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