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FOBI: an ontology to represent food intake data and associate it with metabolomic data

Nutrition research can be conducted by using two complementary approaches: (i) traditional self-reporting methods or (ii) via metabolomics techniques to analyze food intake biomarkers in biofluids. However, the complexity and heterogeneity of these two very different types of data often hinder their...

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Autores principales: Castellano-Escuder, Pol, González-Domínguez, Raúl, Wishart, David S, Andrés-Lacueva, Cristina, Sánchez-Pla, Alex
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7298227/
https://www.ncbi.nlm.nih.gov/pubmed/32556148
http://dx.doi.org/10.1093/databa/baaa033
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author Castellano-Escuder, Pol
González-Domínguez, Raúl
Wishart, David S
Andrés-Lacueva, Cristina
Sánchez-Pla, Alex
author_facet Castellano-Escuder, Pol
González-Domínguez, Raúl
Wishart, David S
Andrés-Lacueva, Cristina
Sánchez-Pla, Alex
author_sort Castellano-Escuder, Pol
collection PubMed
description Nutrition research can be conducted by using two complementary approaches: (i) traditional self-reporting methods or (ii) via metabolomics techniques to analyze food intake biomarkers in biofluids. However, the complexity and heterogeneity of these two very different types of data often hinder their analysis and integration. To manage this challenge, we have developed a novel ontology that describes food and their associated metabolite entities in a hierarchical way. This ontology uses a formal naming system, category definitions, properties and relations between both types of data. The ontology presented is called FOBI (Food-Biomarker Ontology) and it is composed of two interconnected sub-ontologies. One is a ’Food Ontology’ consisting of raw foods and ‘multi-component foods’ while the second is a ‘Biomarker Ontology’ containing food intake biomarkers classified by their chemical classes. These two sub-ontologies are conceptually independent but interconnected by different properties. This allows data and information regarding foods and food biomarkers to be visualized in a bidirectional way, going from metabolomics to nutritional data or vice versa. Potential applications of this ontology include the annotation of foods and biomarkers using a well-defined and consistent nomenclature, the standardized reporting of metabolomics workflows (e.g. metabolite identification, experimental design) or the application of different enrichment analysis approaches to analyze nutrimetabolomic data. Availability: FOBI is freely available in both OWL (Web Ontology Language) and OBO (Open Biomedical Ontologies) formats at the project’s Github repository (https://github.com/pcastellanoescuder/FoodBiomarkerOntology) and FOBI visualization tool is available in https://polcastellano.shinyapps.io/FOBI_Visualization_Tool/.
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spelling pubmed-72982272020-06-22 FOBI: an ontology to represent food intake data and associate it with metabolomic data Castellano-Escuder, Pol González-Domínguez, Raúl Wishart, David S Andrés-Lacueva, Cristina Sánchez-Pla, Alex Database (Oxford) Original Article Nutrition research can be conducted by using two complementary approaches: (i) traditional self-reporting methods or (ii) via metabolomics techniques to analyze food intake biomarkers in biofluids. However, the complexity and heterogeneity of these two very different types of data often hinder their analysis and integration. To manage this challenge, we have developed a novel ontology that describes food and their associated metabolite entities in a hierarchical way. This ontology uses a formal naming system, category definitions, properties and relations between both types of data. The ontology presented is called FOBI (Food-Biomarker Ontology) and it is composed of two interconnected sub-ontologies. One is a ’Food Ontology’ consisting of raw foods and ‘multi-component foods’ while the second is a ‘Biomarker Ontology’ containing food intake biomarkers classified by their chemical classes. These two sub-ontologies are conceptually independent but interconnected by different properties. This allows data and information regarding foods and food biomarkers to be visualized in a bidirectional way, going from metabolomics to nutritional data or vice versa. Potential applications of this ontology include the annotation of foods and biomarkers using a well-defined and consistent nomenclature, the standardized reporting of metabolomics workflows (e.g. metabolite identification, experimental design) or the application of different enrichment analysis approaches to analyze nutrimetabolomic data. Availability: FOBI is freely available in both OWL (Web Ontology Language) and OBO (Open Biomedical Ontologies) formats at the project’s Github repository (https://github.com/pcastellanoescuder/FoodBiomarkerOntology) and FOBI visualization tool is available in https://polcastellano.shinyapps.io/FOBI_Visualization_Tool/. Oxford University Press 2020-06-17 /pmc/articles/PMC7298227/ /pubmed/32556148 http://dx.doi.org/10.1093/databa/baaa033 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Castellano-Escuder, Pol
González-Domínguez, Raúl
Wishart, David S
Andrés-Lacueva, Cristina
Sánchez-Pla, Alex
FOBI: an ontology to represent food intake data and associate it with metabolomic data
title FOBI: an ontology to represent food intake data and associate it with metabolomic data
title_full FOBI: an ontology to represent food intake data and associate it with metabolomic data
title_fullStr FOBI: an ontology to represent food intake data and associate it with metabolomic data
title_full_unstemmed FOBI: an ontology to represent food intake data and associate it with metabolomic data
title_short FOBI: an ontology to represent food intake data and associate it with metabolomic data
title_sort fobi: an ontology to represent food intake data and associate it with metabolomic data
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7298227/
https://www.ncbi.nlm.nih.gov/pubmed/32556148
http://dx.doi.org/10.1093/databa/baaa033
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