FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration

Damion M Dooley,Robert Hoehndorf,Gurinder S Gosal,Matthew C Lange,Emma J Griffiths,William W L Hsiao,Pier L Buttigieg,Lynn M Schriml,Fiona S L Brinkman

doi:10.1038/s41538-018-0032-6

Abstract

The construction of high capacity data sharing networks to support increasing government and commercial data exchange has highlighted a key roadblock: the content of existing Internet-connected information remains siloed due to a multiplicity of local languages and data dictionaries. This lack of a digital lingua franca is obvious in the domain of human food as materials travel from their wild or farm origin, through processing and distribution chains, to consumers. Well defined, hierarchical vocabulary, connected with logical relationships—in other words, an ontology—is urgently needed to help tackle data harmonization problems that span the domains of food security, safety, quality, production, distribution, and consumer health and convenience. FoodOn (http://foodon.org) is a consortium-driven project to build a comprehensive and easily accessible global farm-to-fork ontology about food, that accurately and consistently describes foods commonly known in cultures from around the world. FoodOn addresses food product terminology gaps and supports food traceability. Focusing on human and domesticated animal food description, FoodOn contains animal and plant food sources, food categories and products, and other facets like preservation processes, contact surfaces, and packaging. Much of FoodOn’s vocabulary comes from transforming LanguaL, a mature and popular food indexing thesaurus, into a World Wide Web Consortium (W3C) OWL Web Ontology Language-formatted vocabulary that provides system interoperability, quality control, and software-driven intelligence. FoodOn compliments other technologies facilitating food traceability, which is becoming critical in this age of increasing globalization of food networks.

Highlights

Digital technology innovation is profoundly affecting many health and economic aspects of food production, distribution, and consumption
The authors point out the difficulty in achieving cross-cultural and expert consensus about the structure of term hierarchies in use case domains like nutrient content, culinary use, biological taxonomy, and health research with respect to packaging and food additives
Reuse of terms allows the effort of providing standardized vocabulary to be shared; so for example, FoodOn has replaced about 600 LanguaL chemicals with ChEBI ontology chemical identifiers.[16]

Summary

INTRODUCTION

Digital technology innovation is profoundly affecting many health and economic aspects of food production, distribution, and consumption. Reuse of terms allows the effort of providing standardized vocabulary to be shared; so for example, FoodOn has replaced about 600 LanguaL chemicals (e.g., food additives) with ChEBI ontology chemical identifiers.[16] OBO Foundry ontologies must aspire to a certain overall technical structure, including the upper-level Basic Formal Ontology, curation best practices that involve versioning of ontology files, permanent URLS for terms, and a scheme for annotating deprecated terms’ replacements so that database content can be updated smoothly.[17]. This is accomplished using a python script that uses the rdflib module to read an ontology into memory as an RDF graph of triples, and uses SPARQL to query it and convert it into a JSON representation which the GEEM web interface renders as HTML forms or downloadable specifications

DISCUSSION

METHODS

11. LanguaL 2000