=Paper=
{{Paper
|id=Vol-1747/IP21_ICBO2016
|storemode=property
|title=FoodON: A Global Farm-to-Fork Food Ontology
|pdfUrl=https://ceur-ws.org/Vol-1747/IP21_ICBO2016.pdf
|volume=Vol-1747
|authors=Emma Griffiths,Damion Dooley,Pier Luigi Buttigieg,Robert Hoehndorf,Fiona Brinkman,William Hsiao
|dblpUrl=https://dblp.org/rec/conf/icbo/GriffithsDBHBH16
}}
==FoodON: A Global Farm-to-Fork Food Ontology ==
https://ceur-ws.org/Vol-1747/IP21_ICBO2016.pdf
FoodON: A Global Farm-to-Fork Food Ontology
The Development of a Universal Food Vocabulary
Emma Griffiths, Fiona Brinkman Damion Dooley, Will Hsiao
Department of Molecular Biology and Biochemistry BC Public Health Laboratory
Simon Fraser University Vancouver, Canada
Greater Vancouver, Canada
Robert Hoehndorf
Pier Buttigieg Department of Computer Science
Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und King Abdullah University
Meeresforschung Thuwal, Saudi Arabia
Bremerhaven, Germany
Abstract— Several resources and standards for indexing food have major impacts in many aspects of life, from cultural
descriptors currently exist, but their content and interrelations are practices to purchasing and economics to health and safety.
not semantically and logically coherent. Simultaneously, the need Many food vocabularies have been developed to meet local
to represent knowledge about food is central to many fields needs, but differences in their content, structure and purpose
including biomedicine and sustainable development. FoodON is a limit their global adoption. As such, these resources conflict
new ontology built to interoperate with the OBO Library and to when information must be shared on a broader basis. A food
represent entities which bear a “food role”. It encompasses ontology which seeks to harmonize the semantics behind these
materials in natural ecosystems and food webs as well as human- vocabularies would standardize information transfer between
centric categorization and handling of food. The latter will be the
national and international organizations, and allow integration
initial focus of the ontology, and we aim to develop semantics for
food safety, food security, the agricultural and animal husbandry
of diverse data entities.
practices linked to food production, culinary, nutritional and II. DEVELOPMENT OF THE FOODON FOOD ONTOLOGY
chemical ingredients and processes. The scope of FoodON is
ambitious and will require input from multiple domains. A. Potential Use Cases for a Global Food Ontology
FoodON will import or map to material in existing ontologies and
standards and will create content to cover gaps in the Initial interviews with domain experts (public health agencies,
representation of food-related products and processes. As a robust food allergy strategy committee members, agriculture and agri-
food ontology can only be created by consensus and wide adoption, food specialists, US Food and Drug Administration officials
we are currently forming an international consortium to build etc) have suggested a number of use cases for which a global
partnerships, solicit domain expertise, and gather use cases to food ontology will have immediate and considerable impact.
guide the ontology’s development. The products of this work are These use cases include food safety (source attribution during
being applied to research and clinical datasets such as those
outbreaks, contamination traceback, risk assessment), food
associated with the Canadian Healthy Infant Longitudinal
Development (CHILD) study which examines the causal factors of
security (production, storage, processing, distribution,
asthma and allergy development in children, and the Integrated consumption), food allergy, chemical exposure and nutritional
Rapid Infectious Disease Analysis (IRIDA) platform for genomic assessment, food regulation, trade (import/export/economics),
epidemiology and foodborne outbreak investigation. cultural practices, cooking and culinary use, food webs/food
cycles and animal husbandry. An example of how a food
Keywords—food ontology, food safety, food security, food ontology would have immediate impact is in resolving
allergy, nutrition discrepancies arising from food synonyms (e.g. cold cuts vs
I. INTRODUCTION deli meats). Such discrepancies can obscure query results and
have important consequences in real-time investigations. We
All living things require food to survive. While some will use these use cases to guide development and test the
organisms can utilize sunlight and chemicals to synthesize their competencies of FoodON as it develops.
own nutrients, all animals require exogenous food sources. Food
is such a critical resource for life that a substantial proportion of B. Harmonization of Existing Food Vocabularies
time and effort in an animal’s life is spent procuring it. Humans Several resources and standards for indexing food descriptors
have built intricate systems for the production, distribution, currently exist. The Codex Alimentarius is a collection of
acquisition, regulation, treatment, consumption and disposal of internationally recognized standards, codes of practice,
food. The relationships between humans and food are complex, guidelines, and other recommendations relating to foods, food
and have real consequences for policy, security, education and
production, and food safety commissioned by the United
science. The ways in which we communicate about food can
This work was supported by Genome Canada and Genome BC.
Nations Food and Agriculture Organization III. FORMATION OF THE FOODON CONSORTIUM
(http://www.fao.org/fao-who-codexalimentarius/codex- The creation of such a Food Ontology is a large undertaking
home/en/). LanguaL, or the Langua aLimentaria [1], was first and is much more tractable through an open-member consortium
developed in the late seventies by USFDA’s Centre for Food framework. As harmonization of the food ontology can only be
Safety and Applied Nutrition, and is now hosted by a achieved by consensus and wide adoption, we are currently
consultancy, Danish Food Informatics, on behalf of various forming an international consortium to build partnerships and
European partners. LanguaL provides 14 main facets, or solicit domain expertise. An open-membership consortium will
hierarchies of descriptive terms that have been used to describe be key to developing a sustainable and extensible FoodON.
around 35,000 foods. It has been internationalized with Priorities of the consortium include term contributions,
equivalent terms in Czech, Danish, English, French, German, integration of regionally-specific food vocabulary and strategies
Italian, Portuguese, Spanish and Hungarian. Europe is also for international uptake. Subsets of FoodON will be utilized by
home to FoodEx [2], a food dictionary constructed by the the Integrated Rapid Infectious Disease Analysis (IRIDA)
European Food Safety Authority (EFSA). The latest version platform which supports real-time foodborne outbreak
(Food Ex2) provides a comprehensive classification of terms investigation, as part of the Genomic Epidemiology Application
and is designed to facilitate food exposure assessment. Other Ontology (GenEpiO, www.irida.ca). FoodON vocabulary will
related resources include the USDA National Nutrient Database also be useful for standardizing food descriptions within the
for Standard Reference [3], and the Health Canada Canadian Healthy Infant Longitudinal Development (CHILD)
study, which examines the causal factors of asthma and allergy
Compendium of Analytical Methods, designed to foster
development in children. Interested participants should contact
compliance of the food industry with standards and guidelines the authors for further details.
relative to microbiological and extraneous material in foods [4].
Ontological representation of food products is somewhat REFERENCES
scattered and not comparably comprehensive. For example, [1] Ireland JD & Møller A (2010). LanguaL food description: a
following requests from its users due to the lack of an learning process. Eur J Clin Nutr. 64 Suppl 3:S44-8.
independent food ontology, the Environment Ontology
(ENVO) contained representations of a range of food products [2] European Food Safety Authority (2015). The food
[5]. The experimental FoodO ontology was designed to classification and description system FoodEx2 (revision 2).
represent the FooDB database describing food items and EFSA supporting publication 2015:EN-804. 90 pp.
chemical/nutritional composition (http://aber- [3] Ahuja JK, Moshfegh AJ, Holden JM & Harris E (2013).
owl.net/ontology/FOODO). While these resources are certainly USDA food and nutrient databases provide the infrastructure for
useful, they have only been developed for specific uses and food and nutrition research, policy, and practice. J Nutr.
often include different facets and organizational principles. 143(2):241S-9S.
These features limit interoperability and reduce the range of
[4] Health Canada (2011). “Guidelines for the Relative
application an integrative and semantically coherent food
Validation of Indirect Qualitative Food Microbiological
ontology would possess. Methods” in The Compendium of Analytical Methods (Vol 1).
[5] Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE
C. FoodON Structure and Content & the ENVO Consortium (2013). The environment ontology:
We are developing FoodON following the principles of the contextualising biological and biomedical entities. J Biomed
OBO Foundry and Library [6]. Its upper levels will be Semantics. 4(1):43.
concerned with food composition, pre-collection (farming or
[6] Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters
animal husbandry) environment, collection features (season, W, Goldberg LJ, Eilback K, Ireland A, Mungall CJ, The OBI
age of plant or animal, harvesting technology), storage and Consortium, Leontis N, Rocca-Serra P, Ruttenberg A,Sansone
distribution features as they pertain to food security, culinary S-A, Scheuermann RH, Shah N, Whetzel PL & Lewis S (2007).
preparation and packaging, food safety factors, and The OBO Foundry: coordinated evolution of ontologies to
consumption patterns. Food-relevant terms are being imported support biomedical data integration. Nat Biotechnol. 25(11):
from existing ontologies including NCBI Taxonomy for source 1251-5. http://doi.org/10.1038/nbt1346
animal / plant / fungi / bacterial organism, Uberon [7] for food
source part and type descriptors, ENVO for food environmental [7] Mungall CJ, Torniai C, Gkoutos GV, Lewis SE & Haendel
MA (2012). Uberon, an integrative multi-species anatomy
context, and CHEBI [8] for chemical constituents and
ontology. Genome Biol. 13(1), R5. http://doi.org/10.1186/gb-
contaminants. LanguaL, a traditional database, will be used for
2012-13-1-r5
food source common names, preservation methods, and a few
other facets. The ontology is open and available on GitHub [8] Degtyarenko K, de Matos P, Ennis M, Hadtings J, Zbinden
(https://github.com/FoodOntology) such that editors, each with M, McNaught A, Alcantara R, Darsow M, Guedj M &
their own allotment of term identifiers, can effectively Ashburner M (2008). ChEBI: a database ontology for chemical
contribute in parallel and the community can submit term entities of biological interest. Nucleic Acids Res. 36 (Database
requests and feedback. issue), D344-50. http://doi.org/10.1093/nar/gkm791
This work was supported by Genome Canada and Genome BC.