ONS: an ontology for a standardized description of interventions and observational studies in nutrition

Human Nutritional Science studies the effects of food components on metabolism, health, performance, and disease resistance of humans, also encompassing the study of human behavior related to food choices. Nutritional epidemiology, on the other hand, assesses the relations between diet, nutrients and health, and disease outcomes [1]. Yet, there is a major disconnection between the description of nutrition-based prevention of disease and the understanding of the complex network of interactions by which nutrition modulates health. To fill this gap, a set of nutrition-related sub-disciplines (e.g., nutritional biochemistry, clinical nutrition, nutritional epidemiology, nutrigenetics, and nutrimetabolomics) provide fundamental evidence at different levels and from different perspectives, contributing to the expansion of nutritional science as a more systematic and complex discipline [2, 3]. As nutrition data are heterogeneous in terms of quality and nature, a comprehensive consideration of all aspects is challenging [4], even if substantial advance has been made to improve the reporting of findings and the data quality [5] of nutrition research [6], which is one of the prerequisites for integrated analysis.

To integrate evidence, a systematic re-organization of concept definitions is needed. Currently, concept definitions are often derived from multiple sources, with the drawback that slight variations can lead to misleading interpretations [7]. Since in bioscience in general, and in nutritional science in particular, the same concept can be referred to by multiple synonymous terms, abbreviations, or acronyms [8], as well as using different languages, term classifications such as the Medical Subject Headings (MeSH) [9] or the NCI Thesaurus [10] provide fundamental resources. However, thesauri or controlled vocabularies for biomedical information do not specify relations between concepts. Although those efforts can be used to standardize general study descriptions, considerable advances would arise from the use of resources that, in addition to standardizing the vocabulary, also include connections/relations between classes, such as ontologies, specifically tailored to the nutritional sciences.

Often biomedical researchers refer to ontologies using the terminologies more appropriately pertaining to “controlled vocabularies,” “thesauri” (i.e., a list, often organized in a hierarchy or taxonomy, of concepts and their textual descriptions), or “taxonomies” (i.e., a hierarchy consisting of terms denoting classes linked by sub- and super-class relations). A proper ontology, however, is defined as a formal representation of knowledge in a certain reality (i.e., a certain domain of knowledge), in a way that different people—and, notably, computers—can understand the concepts it contains and learn about the reality that is being represented [8, 11]. Ontologies consist of defined classes of entities, typically structured within a knowledge hierarchy where concepts are connected by standardized [12] semantic relationships (i.e., “is-a,” “part-of”) formally specifying knowledge relations such as generalizations of specifications of the reality of interest [13].

Open Biomedical Ontologies (OBO), established in 2001, is a platform for developing interoperable ontologies for biomedical research [14]. Efforts have been made in the agricultural field to develop nutrition-oriented ontologies focused on the description of food components such as “the food classification and description system” [15] developed by European Food Safety Authority (EFSA). Other notable efforts in developing food-focused ontologies were reviewed elsewhere [16]. Based on literature search and public ontological repository queries (OBO Foundry searched using ONTOBEE, and Bioportal), a single example of a nutritional ontology was found (the Bionutrition Ontology—BNO, http://purl.bioontology.org/ontology/BNO). The latter represents a controlled vocabulary of nutritional terms, without a proper annotation of terms or definition of properties, and lacks orthogonality (i.e., no terms are imported or refer to external ontologies). To the authors’ knowledge, a proper ontology integrating the terms related to food description, medical science, genetics, genomics data, and nutritional science methods for diet and health research is not available to date. To fill this gap, we present the Ontology for Nutritional Studies (ONS) to facilitate the harmonization and integration of biological samples collected using different methodologies, referred to by differing terminologies in various fast-growing sub-disciplines in the dietary and health research.

The ONS was developed within the European Nutritional Phenotype Assessment and Data Sharing Initiative (ENPADASI) consortium [17], which joins scientists from 51 research centers in nine countries of Europe with the common effort to handle and make available big nutritional data through the open access nutritional database Data Sharing In Nutrition (DASH-IN) [17, 18]. DASH-IN is a distributed pan-European infrastructure and supports the storage of both interventional and observational studies and provides the tools for distributed management and search and analysis of the data [19]. The development of this infrastructure requires an ontology to harmonize biochemical, genetic, clinical, and nutritional concepts typically found in intervention and observational studies. The ontology would provide a coherent means of data annotation and data querying over the distributed infrastructure. Further developments of the project led to a stronger need for a proper conceptual framework such as the ONS that could be used by a broader nutrition community to build upon for annotating general nutritional studies. The ENPADASI framework gathered researchers from different nutrition-related fields (health sciences, biology, genetics, microbiology, agricultural sciences, food technology, science of materials, chemistry, metabolomics, genomics, bioinformatics, and metagenomics) and offered the ideal milieu for creating the first ontology in nutrition.

Terms to be included in the ONS were collected among partners of the ENPADASI consortium, as well as from templates for data and metadata upload into the DASH-IN databases. In compliance with the OBO Foundry principles [14], the ONS has been developed to be as follows: (i) Interoperable with other ontologies, as it has been formalized using the latest OWL 2 Web Ontology Language [20] and RDF specifications [21] and edited using Protégé [22]; the hermit reasoner (http://hermit-reasoner.com/) was used for consistency checking. (ii) Accessible, under the Creative Commons license (CC BY 4.0), published on GitHub (https://github.com/enpadasi/Ontology-for-Nutritional-Studies) and at NCBO BioPortal (http://bioportal.bioontology.org/ontologies/ONS). (iii) Orthogonal to other ontologies by reusing existing terms. Besides assuring compliance with the OBO Foundry principles, we also ensured that the ONS followed the increasingly established FAIR principles [23]. As such, the ONS is also published in the FAIRsharing database (https://fairsharing.org/bsg-s001068).

To enhance interoperability with other ontologies, the ONS builds on a subset of the Ontology for Biomedical Investigations (OBI) [24]. The subset was created using the ONTODOG tool [25] and is composed of all terms relevant to nutritional investigations and extended also in accordance with the bioinformatics infrastructure of ENPADASI. Moreover, this assured the adoption of a well-defined and widely adopted structure for the top and mid-level classes and principally the adherence to the Basic Formal Ontology (BFO) [26] as upper ontology.

The initial ontological curation identified a large number of relevant terms to consider. The terms were then either imported from existing ontologies, redefined from existing concepts, or annotated de novo. By merging 3334 terms imported from already existing ontologies and 100 newly defined terms, the ONS describes both intervention and observational studies in nutrition.

Central nutritional concepts

In the ONS, relevant nutritional concepts have been related to each other to offer a well-organized synopsis of the knowledge in health and nutrition sciences. The ONS harmonizes all pertinent concepts from different domains, defining appropriate relationships and improving and simplifying the process of conceptual organization of the many facets of real studies. Here, we present (Fig. 1) how diet, food, and food component concepts, which can be considered central for an ontology aimed at effectively assisting researchers in the standardized description of the nutritional study they are conducting, were included, defined, and connected in the ONS.

Diet is defined as the regular course of eating and drinking adopted by a person or animal (ONS_0000080). For the purpose of the nutritional community, we further detailed the diet concept into three sub-classes: (i) Usual diet is defined as the regular course of eating and drinking adopted by a population in a certain geographical area, or in a certain cultural setting, or following certain common eating behavior. It is also intended as the diet a person would follow without further prescription or indications, i.e., vegetarian diet (ONS_0000083). (ii) Prescribed diet is defined as a diet prescribed by a physician/nutritionist to meet specific nutritional needs of a person (ONS_0000082). (iii) Intervention diet is defined as the diet administered during an intervention study. It usually comprises the adoption of a certain nutritional intervention (ERO_0000347), intended as the prescription of consuming or not consuming certain food, and follows a precise study design. Intervention studies usually compare at least two subgroups of a population, one control group receiving a null nutritional intervention and one or more test groups receiving the intervention (ONS_0000081).

Food component is defined as any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants (CHEBI_78295, ONS_0000073). Starting from this definition, we further detailed the food component concept into different sub-classes: (i) Nutrient (ONS_0000077): A nutrient is a food component used by the body for normal physiological functions that guarantee survival and growth. It must be supplied in adequate and defined amounts from foods consumed within a diet. Malnutrition occurs when the right amount of nutrient is not provided. (ii) Food bioactive (ONS_0000076): A food bioactive is a food component other than those needed to meet basic human nutritional needs (nutrients). Food bioactives modulate one or more metabolic processes, possibly resulting in the promotion of better health. The daily required intake for food bioactives is not established yet, and there is no demonstration that malnutrition occurs when the right amount is not provided. (iii) Contaminant: Contaminant is unwanted food component that makes the food no longer suitable for use (ONS_0000075). (iv) Additive: Additive is a component added to food to improve or preserve it (ONS_0000074).

Multiple definitions can be found for the food concept. As an example, CHEBI (CHEBI:33290) defines “Any material that can be ingested by an organism” and MESH (MeSH D005502) defines “Any substances taken in by the body that provides nourishment.” For the purposes of the nutritional community, the concept of food was expanded as food is defined as a complex matrix that is consumed by a person through the process of eating or drinking (ONS_0000079). Foods are bearer of the nutrients, bioactives, and, sometimes, other food components. Food consumption, through the meal consumption, follows a certain dietary pattern, which define the diet. Nutrients and bioactives contained in food can be exploited by the human organism thanks to the process of digestion (ONS_0000101), absorption (ONS_0000102), metabolization (ONS_0000103), or through the intervention of the gut microflora (OHMI_0000020). The concept of food can be split into the following: (i) Raw food: A raw food is an uncooked, unprocessed food that is consumed in its natural state (ONS_0000099); (ii) Processed food: A processed food is the result of the process of home or industrial food preparation (ONS_0000100).

In nutritional science, biomarkers are increasingly being used to provide objective results and to avoid biases (e.g., reporting bias and recall bias). Three groups of biomarkers were identified for use in nutrition science [30], along with the dietary biomarker development framework: “exposure biomarker” for dietary intake and nutrient status, “effect biomarker” for measuring biological effects of food components, and “susceptibility biomarker” for assessing the effects of diet on human health. In the ONS, we are presenting the first formal ontology application for the biomarker class (ONS_0000095) and its sub-classes, using the definition from the commentary [30]. ONTOBEE query for the “biomarker” returned multiple results mainly from the Experimental Factor Ontology (EFO), all having the class “Measurement” (EFO_0001444) as super-class (a measurement is an information entity that is a recording of the output of a measurement such as produced by an instrument). However, it has to be noted that a similar class can also be found in the Information Artifact Ontology (IAO) named “Measurement datum” (IAO_0000109, a measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device). In the ONS, the biomarker class was defined as a sub-class of the “Measurement datum” class (IAO_0000109) in line with the OBI ontology, which uses the IAO class.

Integrated analysis of data and joint pooled analysis are strongly promoted in nutrition by research funders, though raise scientists’ concern, as the scientific interest in the open access to nutritional data often conflicts with the General Data Protection Regulation. When fully achieved, integrated analysis will lead to new discoveries and maximize use of public funds. In ENPADASI, this problem was broadly dealt with from both legal and technical aspects, and a recommendation on minimal information to be added as metadata to studies to boost integration capacity has been developed [19]. The identification of minimal requirements, essential to connect existing and future study (meta) databases, facilitates data exchange and data interpretation, helping to increase the robustness of results from future joint data analysis in nutritional epidemiology [31]. In fact, joint data analysis has already started helping to achieve new discoveries [32]. In the ONS, we have included the minimal required study information in the growing conceptual/ontological framework. Each minimal required study term was placed at the appropriate hierarchical level in the ontology. To easily identify terms pertaining to the minimal study information, an annotation property (“in_minimal_requirements_subset”) was created.

Application scenarios

The ONS is designed to enable the description of both intervention and observational studies in human nutrition. Here, we present two application scenarios based on published nutritional studies, one for the observational study design and one for the interventional study design. Figures 2 and 3 illustrate how the ONS was built to support the standardized annotation of most descriptors of a nutritional study, starting from initial phases of a study (i.e., formalizing the definition of population stratum) to finally connect to the specific results and how they were obtained. Figures and descriptions have to be intended at the single instance level (i.e., specific for the study object of description). For this reason, we introduced the use of individuals (and their connections) for very study-specific element alongside concepts in classes. In the text below, the italic notation indicates the properties, while the notation PREFIX:CLASS is used to indicate classes in the ontology, for example the notation “ONS:Diet” indicates the class with label “Diet” in the ONS ontology. For abbreviation of the ontologies, we refer the reader to the list of imported ontologies in the “Methods” section.

The ONS is the first systematic effort to provide a formal ontology framework for the description of nutritional studies. In this context, the main aim of the ONS is the establishment of an ontological framework that can assist nutrition researchers by selecting the appropriate terms from the wide range of existing ontologies and creating the relevant missing key concepts for the field. Nutrition researchers, who might not necessarily be familiar with ontologies and concept standardization, can find in the ONS a single knowledge entry point for a unified and standardized terminology without having to resort to numerous ontology sources. In addition to standardizing concept descriptions and assisting in annotation, the ONS will structure querying of nutritional studies stored in public databases (such as the resources developed in the ENPADASI project). Finding the suitable studies (i.e., those more directly comparable regarding design, employed stratification criteria, or type of intervention diet employed) represents the basis for integrated analysis. Such a query, in fact, cannot be efficiently based on string matching, but rather on more complex textual analysis and machine learning methodologies for which ontology is crucial. A well-established nutritional ontology would also enable more accurate search for required data as well as the automated integration and analysis of data from multiple sources [36].

Diet, nutrient, and food are indeed central concepts for nutritional sciences, and they were included and connected with higher level concepts in ONS. Moreover, the ONS supports the research needs identified by other initiatives such as the Food Biomarkers Alliance (FoodBAll) by including for the first time in a formal ontology the concept of biomarker in nutrition, and its sub-classes, as defined in [30].

Besides acquiring widespread utilization, an ontology can be considered successful only if (i) continuous development and (ii) constant contribution/updates from researchers with specific knowledge is ensured. We invite and encourage researchers in the nutritional field to contribute to the further development, adoption, and promotion of the ONS. Contributions are already possible using the GitHub tracking/issues system (Additional file 1) and an online community platform to facilitate the process of curation and extension of the ONS will be developed for this purpose. As a next challenge, the ONS aims to integrate nutritional studies with non-life sciences such as economy, psychology, and sociology, which also influence the nutritional status of individuals [37–39].