Smell compounds classification using UMAP to increase knowledge of odors and molecular structures linkages.

This study aims to highlight the relationships between the structure of smell compounds and their odors. For this purpose, heterogeneous data sources were screened, and 6038 odorant compounds and their known associated odors (162 odor notes) were compiled, each individual molecule being represented...

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Autores principales:	Marylène Rugard, Thomas Jaylet, Olivier Taboureau, Anne Tromelin, Karine Audouze
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/717ae7952f034139937a973f203b5594
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spelling	oai:doaj.org-article:717ae7952f034139937a973f203b55942021-12-02T20:11:12ZSmell compounds classification using UMAP to increase knowledge of odors and molecular structures linkages.1932-620310.1371/journal.pone.0252486https://doaj.org/article/717ae7952f034139937a973f203b55942021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0252486https://doaj.org/toc/1932-6203This study aims to highlight the relationships between the structure of smell compounds and their odors. For this purpose, heterogeneous data sources were screened, and 6038 odorant compounds and their known associated odors (162 odor notes) were compiled, each individual molecule being represented with a set of 1024 structural fingerprint. Several dimensional reduction techniques (PCA, MDS, t-SNE and UMAP) with two clustering methods (k-means and agglomerative hierarchical clustering AHC) were assessed based on the calculated fingerprints. The combination of UMAP with k-means and AHC methods allowed to obtain a good representativeness of odors by clusters, as well as the best visualization of the proximity of odorants on the basis of their molecular structures. The presence or absence of molecular substructures has been calculated on odorant in order to link chemical groups to odors. The results of this analysis bring out some associations for both the odor notes and the chemical structures of the molecules such as "woody" and "spicy" notes with allylic and bicyclic structures, "balsamic" notes with unsaturated rings, both "sulfurous" and "citrus" with aldehydes, alcohols, carboxylic acids, amines and sulfur compounds, and "oily", "fatty" and "fruity" characterized by esters and with long carbon chains. Overall, the use of UMAP associated to clustering is a promising method to suggest hypotheses on the odorant structure-odor relationships.Marylène RugardThomas JayletOlivier TaboureauAnne TromelinKarine AudouzePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 5, p e0252486 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Marylène Rugard Thomas Jaylet Olivier Taboureau Anne Tromelin Karine Audouze Smell compounds classification using UMAP to increase knowledge of odors and molecular structures linkages.
description	This study aims to highlight the relationships between the structure of smell compounds and their odors. For this purpose, heterogeneous data sources were screened, and 6038 odorant compounds and their known associated odors (162 odor notes) were compiled, each individual molecule being represented with a set of 1024 structural fingerprint. Several dimensional reduction techniques (PCA, MDS, t-SNE and UMAP) with two clustering methods (k-means and agglomerative hierarchical clustering AHC) were assessed based on the calculated fingerprints. The combination of UMAP with k-means and AHC methods allowed to obtain a good representativeness of odors by clusters, as well as the best visualization of the proximity of odorants on the basis of their molecular structures. The presence or absence of molecular substructures has been calculated on odorant in order to link chemical groups to odors. The results of this analysis bring out some associations for both the odor notes and the chemical structures of the molecules such as "woody" and "spicy" notes with allylic and bicyclic structures, "balsamic" notes with unsaturated rings, both "sulfurous" and "citrus" with aldehydes, alcohols, carboxylic acids, amines and sulfur compounds, and "oily", "fatty" and "fruity" characterized by esters and with long carbon chains. Overall, the use of UMAP associated to clustering is a promising method to suggest hypotheses on the odorant structure-odor relationships.
format	article
author	Marylène Rugard Thomas Jaylet Olivier Taboureau Anne Tromelin Karine Audouze
author_facet	Marylène Rugard Thomas Jaylet Olivier Taboureau Anne Tromelin Karine Audouze
author_sort	Marylène Rugard
title	Smell compounds classification using UMAP to increase knowledge of odors and molecular structures linkages.
title_short	Smell compounds classification using UMAP to increase knowledge of odors and molecular structures linkages.
title_full	Smell compounds classification using UMAP to increase knowledge of odors and molecular structures linkages.
title_fullStr	Smell compounds classification using UMAP to increase knowledge of odors and molecular structures linkages.
title_full_unstemmed	Smell compounds classification using UMAP to increase knowledge of odors and molecular structures linkages.
title_sort	smell compounds classification using umap to increase knowledge of odors and molecular structures linkages.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/717ae7952f034139937a973f203b5594
work_keys_str_mv	AT marylenerugard smellcompoundsclassificationusingumaptoincreaseknowledgeofodorsandmolecularstructureslinkages AT thomasjaylet smellcompoundsclassificationusingumaptoincreaseknowledgeofodorsandmolecularstructureslinkages AT oliviertaboureau smellcompoundsclassificationusingumaptoincreaseknowledgeofodorsandmolecularstructureslinkages AT annetromelin smellcompoundsclassificationusingumaptoincreaseknowledgeofodorsandmolecularstructureslinkages AT karineaudouze smellcompoundsclassificationusingumaptoincreaseknowledgeofodorsandmolecularstructureslinkages
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Smell compounds classification using UMAP to increase knowledge of odors and molecular structures linkages.

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