- Several resources and standards for indexing food descriptors currently exist, but their content and interrelations are not semantically and logically coherent. Simultaneously, the need to represent knowledge about food is central to many fields including biomedicine and sustainable development. FoodON is a new ontology built to interoperate with the OBO Library and to represent entities which bear a “food role”. It encompasses materials in natural ecosystems and food webs as well as humancentric categorization and handling of food. The latter will be the initial focus of the ontology, and we aim to develop semantics for food safety, food security, the agricultural and animal husbandry practices linked to food production, culinary, nutritional and chemical ingredients and processes. The scope of FoodON is ambitious and will require input from multiple domains. FoodON will import or map to material in existing ontologies and standards and will create content to cover gaps in the representation of food-related products and processes. As a robust food ontology can only be created by consensus and wide adoption, we are currently forming an international consortium to build partnerships, solicit domain expertise, and gather use cases to guide the ontology's development. The products of this work are being applied to research and clinical datasets such as those associated with the Canadian Healthy Infant Longitudinal Development (CHILD) study which examines the causal factors of asthma and allergy development in children, and the Integrated Rapid Infectious Disease Analysis (IRIDA) platform for genomic epidemiology and foodborne outbreak investigation.
All living things require food to survive. While some organisms can utilize sunlight and chemicals to synthesize their own nutrients, all animals require exogenous food sources. Food is such a critical resource for life that a substantial proportion of time and effort in an animal’s life is spent procuring it. Humans have built intricate systems for the production, distribution, acquisition, regulation, treatment, consumption and disposal of food. The relationships between humans and food are complex, and have real consequences for policy, security, education and science. The ways in which we communicate about food can
II. DEVELOPMENT OF THE FOODON FOOD ONTOLOGY A. Potential Use Cases for a Global Food Ontology Initial interviews with domain experts (public health agencies, food allergy strategy committee members, agriculture and agrifood specialists, US Food and Drug Administration officials etc) have suggested a number of use cases for which a global food ontology will have immediate and considerable impact. These use cases include food safety (source attribution during outbreaks, contamination traceback, risk assessment), food security (production, storage, processing, distribution, consumption), food allergy, chemical exposure and nutritional assessment, food regulation, trade (import/export/economics), cultural practices, cooking and culinary use, food webs/food cycles and animal husbandry. An example of how a food ontology would have immediate impact is in resolving discrepancies arising from food synonyms (e.g. cold cuts vs deli meats). Such discrepancies can obscure query results and have important consequences in real-time investigations. We will use these use cases to guide development and test the competencies of FoodON as it develops.
B. Harmonization of Existing Food Vocabularies
Several resources and standards for indexing food descriptors
currently exist. The Codex Alimentarius is a collection of
internationally recognized standards, codes of practice,
guidelines, and other recommendations relating to foods, food
production, and food safety commissioned by the United
Nations Food and Agriculture Organization
(http://www.fao.org/fao-who-codexalimentarius/codexhome/en/). LanguaL, or the Langua aLimentaria [
C. FoodON Structure and Content We are developing FoodON following the principles of the OBO Foundry and Library [6]. Its upper levels will be concerned with food composition, pre-collection (farming or animal husbandry) environment, collection features (season, age of plant or animal, harvesting technology), storage and distribution features as they pertain to food security, culinary preparation and packaging, food safety factors, and consumption patterns. Food-relevant terms are being imported from existing ontologies including NCBI Taxonomy for source animal / plant / fungi / bacterial organism, Uberon [7] for food source part and type descriptors, ENVO for food environmental context, and CHEBI [8] for chemical constituents and contaminants. LanguaL, a traditional database, will be used for food source common names, preservation methods, and a few other facets. The ontology is open and available on GitHub (https://github.com/FoodOntology) such that editors, each with their own allotment of term identifiers, can effectively contribute in parallel and the community can submit term requests and feedback.
The creation of such a Food Ontology is a large undertaking and is much more tractable through an open-member consortium framework. As harmonization of the food ontology can only be achieved by consensus and wide adoption, we are currently forming an international consortium to build partnerships and solicit domain expertise. An open-membership consortium will be key to developing a sustainable and extensible FoodON. Priorities of the consortium include term contributions, integration of regionally-specific food vocabulary and strategies for international uptake. Subsets of FoodON will be utilized by the Integrated Rapid Infectious Disease Analysis (IRIDA) platform which supports real-time foodborne outbreak investigation, as part of the Genomic Epidemiology Application Ontology (GenEpiO, www.irida.ca). FoodON vocabulary will also be useful for standardizing food descriptions within the Canadian Healthy Infant Longitudinal Development (CHILD) study, which examines the causal factors of asthma and allergy development in children. Interested participants should contact the authors for further details. [5] Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE & the ENVO Consortium (2013). The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics. 4(1):43.