The need to represent knowledge about food is central to many human activities including agriculture, medicine, food safety inspection, shopping patterns, and sustainable development. FoodOn is a new ontology built to interoperate with the OBO Library and to represent entities which bear a “food role”. Initially the ontology will focus on the human-centric categorization and handling of food, but in the future it will also encompass materials in natural ecosystems and food webs. 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 imports material from several ontologies covering anatomy, taxonomy, geography and cultural heritage. We aim to create content to cover gaps in the representation of food-related products and processes. This ontology is being applied to research and clinical datasets in academia and government. We also anticipate industry uptake since agricultural and consumer devices connected to the Internet of Things will require a standard food vocabulary that has a global, multilingual reach.
We have launched the ALPHA version of FoodOn, based largely on LanguaL, a descriptive food indexing system that has terms organized in facets that describe source ingredients, food preservation, cooking, consumer groups, etc. (see a great PDF presentation here). Food can also be linked to its cultural or geographic origin, and to its animal, plant or fungi raw ingredient taxonomy. You can view it at the EBI Ontology Lookup Service.
We have begun the process of creating logical definitions for a large number of food products that were introduced by way of the LanguaL-indexed SIREN database (see http://www.langual.org/langual_indexed_datasets.asp). Currently these products are organized manually under the "foodon food product" facet hierarchy, but this will be transformed into an inferred structure as product definitions are updated. An example of more fine-grained axiomatization is shown below, where three different kinds of apple-related products are shown in relation to a food source organism (apple tree) and various food preparation and packaging processes.
FoodOn has LanguaL identifiers for references to all LanguaL food source items and other facet descriptors that FoodOn has imported. However, ontology relations allow us to improve the way components and processes are represented in order to sow the benefits of automated reasoning on food product schemas.
This ontology is now listed with a variety of ontology search engines and retrieval tools:
- National Center for Biomedical Ontology BioPortal
- EMBL-EBI Ontology Lookup Service
- He Group (University of Michigan Medical School) OntoBee
- He Group OntoFox
- LIRMM (University of Montpellier) AgroPortal
Note that as FoodOn is striving to be OBO compatible, its facets or classes are positioned within OBO's upper level ontology.
William Hsiao and Damion Dooley (University of British Columbia Department of Pathology and Laboratory Medicine) and Fiona Brinkman and Emma Griffiths (Simon Fraser University Department of Molecular Biology and Biochemistry) are involved in the IRIDA.ca project with a focus on ontology of food-borne pathogen related (genomic) epidemiology. Fiona and Emma are also involved in The Canadian Healthy Infant Longitudinal Development study (CHILD) investigation of genetic and environmental factors associated with the development of allergy and asthma.
Pier Luigi Buttigieg (Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung) is developing environmental ontologies (ENVO) and semantics for sustainable development. These domains include the semantics of food production, security, and composition.
Robert Hoehndorf (King Abdullah University), a key proponent of the Aber-OWL.net project, is researching chemical exposure with respect to diet and health.
Matthew Lange (UC Davis School of Medicine Department of Physical Medicine and Rehabilitation, and Initiative for Wireless Health and Wellness) spearheads the IC3-Foods consortium, with a focus on the technology and policy implications of next generation food systems.
Lynn Schriml (University of Maryland School of Medicine) is engaged in research on developing bioinformatic tools, metadata standards and ontologies to gain a broader understanding of the relationship between infectious pathogens, their genomic sequence and disease.
As a robust food ontology can only be created by consensus and wide adoption, we are currently forming an international, open-membership consortium to build partnerships, solicit domain expertise, and gather use cases to guide the ontology’s development.