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/.

中文翻译：

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FOBI：表示食物摄入数据并将其与代谢组数据相关联的本体。


营养研究可以通过使用两种互补的方法进行：（i）传统的自我报告方法或（ii）通过代谢组学技术来分析生物体液中的食物摄入生物标志物。然而，这两种截然不同类型的数据的复杂性和异质性常常阻碍它们的分析和集成。为了应对这一挑战，我们开发了一种新颖的本体论，以分层方式描述食物及其相关的代谢实体。该本体使用正式的命名系统、类别定义、属性以及两种类型数据之间的关系。提出的本体称为 FOBI（食品生物标记本体），它由两个互连的子本体组成。一个是“食物本体”，由生食和“多成分食品”组成，而第二个是“生物标记本体”，包含按化学类别分类的食物摄入生物标记。这两个子本体在概念上是独立的，但通过不同的属性相互联系。这使得有关食品和食品生物标志物的数据和信息能够以双向方式可视化，从代谢组学到营养数据，反之亦然。该本体论的潜在应用包括使用明确且一致的命名法对食品和生物标志物进行注释、代谢组学工作流程的标准化报告（例如代谢物鉴定、实验设计）或应用不同的富集分析方法来分析营养代谢组学数据。可用性：FOBI 可以在项目的 Github 存储库 (https://github.com/openbiomedical-ontologies) 上免费获得 OWL（Web 本体语言）和 OBO（开放生物医学本体）格式。com/pcastellanoescuder/FoodBiomarkerOntology）和 FOBI 可视化工具可在 https://polcastellano.shinyapps.io/FOBI_Visualization_Tool/ 中找到。