FoodOn Core Papers
Ontological how and why: action and objective of planned processes in the food domain (2023)
A closer examination of how we consider processes from a how (choice of mechanism), and why (choice of objective) perspective, and how the two get interwoven. A technical rice cooking example is included. https://www.frontiersin.org/articles/10.3389/frai.2023.1137961
OBO Foundry Food Ontology Interconnectivity (2023)
This paper examines recent data interoperability capabilities arising from food-related ontologies belonging to, or compatible with, the encyclopedic Open Biological and Biomedical Ontology Foundry (OBO) ontology platform, and how research organizations and industry might utilize them for their own projects or for data exchange. To satisfy the need for controlled vocabulary across government, industry and research domains involving agriculture, food processing, nutrition and disease, requires establishing domain specific ontologies whose curators coordinate closely to produce recommended patterns for food system vocabulary.
https://www.semantic-web-journal.net/system/files/swj3458.pdf
Food process ontology requirements (2022)
A paper reviewing OBO style process modelling in comparison to SOSA/SSN, OWL-Time, PROVO, and PO2 process related ontologies, culminating in a tentative recipe model that aims to satisfy representation of recipes in both a home and food science context.
English version: https://content.iospress.com/articles/semantic-web/sw223096
A condensed french version, compliments of co-authors at INRAE: https://pfia23.icube.unistra.fr/conferences/ic/publications/IC_2023_paper_34.pdf
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration (2018)
Our inaugural FoodOn paper, available as a pdf at https://rdcu.be/bdLun or on the web at https://www.nature.com/articles/s41538-018-0032-6 .
FDA’s Factored Food Vocabulary for food product description (1975)
A seminal paper that explains the origin – in 1975 – and facets of the Factored Food Vocabulary, which LanguaL and FoodOn are ultimately based on. This paper is available on the LanguaL website.
Food System Related Papers, Articles, Talks
The Food Expiration Dates You Should Actually Follow (2023)
“The dates, as we know them, have nothing to do with safety.”
https://www.nytimes.com/article/expiration-dates-coronavirus.html
The periodic table of fermented foods: limitations and opportunities (2022)
An overview of fermented foods from across the globe. “The periodic table of fermented foods aims to map this diversity on the 118 entries of the periodic table of chemical
elements. While the table fails to represent the diversity of fermented foods, it represents major fermentation substrates, product categories, fermentation processes and fermentation organisms.”
https://pubmed.ncbi.nlm.nih.gov/35412130/
Developing a Dietary Lifestyle Ontology to Improve the Interoperability of Dietary Data: Proof-of-Concept Study
“The main goal of this study was to address the interoperability challenge of questionnaire-based dietary data from different cultural backgrounds by combining ontological curation and metadata annotation of dietary concepts. Specifically, this study aimed to develop a Dietary Lifestyle Ontology (DILON) and demonstrate the improved interoperability of questionnaire-based dietary data by annotating its main semantics with DILON.”
https://www.academia.edu/108491249
How the environment shapes the microbiota in health and disease (2021).
Carolina Tropini discusses principles governing the localization of intestinal bacteria and spatial relationships between bacteria and their hosts, including effects of change in extracellular concentration in the gut of solutes on bacteria cell pressure (osmotic perturbation), a common disturbance caused by food intolerance, malabsorption, and widespread laxative use. The presentation reveals many implications for personalized health and probiotics.
See the one hour video on YouTube.
Food Composition Databases: Does It Matter to Human Health? (2021)
A review of food composition databases worldwide, with a focus as well on the facet description and tagging languages INFOODS, LanguaL, FoodEx2 and FoodOn, used in food description.
https://www.mdpi.com/2072-6643/13/8/2816/pdf
AMALQEIA: A Dish-Driven Ontology in the Food Domain (2021)
An application ontology that models the domain of dishes as they are presented in 112 menus collected from restaurants/taverns/patisseries in East Macedonia and Thrace in Northern Greece, with attention to dietary, geographical and cultural information about the dishes and their ingredients.
https://doi.org/10.3390/data6040041
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research (2021)
The authors review the state of affairs in nutri-informatics data sharing, and “focus on the application of biomedical ontologies and their potential to improve the standardization and interoperability of nutrition terminologies and relationships between nutrition and other biomedical disciplines such as disease and phenomics.”
https://pubmed.ncbi.nlm.nih.gov/33494105/
Perspective: Towards Automated Tracking of Content and Evidence Appraisal of Nutrition Research (2020)
The authors present a semiautomated approach to annotate, link, and track the content of nutrition research manuscripts. It involves the STROBE-nut ontology, crafted to describe and standardize the metadata components of research manuscripts, to manually annotate a sample of 15 articles and converted the semantic information into linked data in a Neo4j graph database through an automated process.
https://academic.oup.com/advances/article/11/5/1079/5854278
Using Word Embeddings to Learn a Better Food Ontology (2020)
A semi-supervised machine learning framework for the automated ontology population from an existing ontology scaffold by using word embeddings. Uses FoodOn structure and a corpus of Wikipedia documents as the training set.
https://www.frontiersin.org/articles/10.3389/frai.2020.584784/full
Common Data Models and Semantic Interoperability Mechanisms (2020)
A report by the Demeter project on the European agri-food sector and pertinent IoT technology.
https://h2020-demeter.eu/wp-content/uploads/2020/10/DEMETER_D21_final.pdf
FOBI: an ontology to represent food intake data and associate it with metabolomic data (2020)
A novel ontology that describes food and its associated metabolite entities in a hierarchical way. This ontology uses a formal naming system, category definitions, properties and relations between both types of data.
https://pubmed.ncbi.nlm.nih.gov/32556148/
Knowledge representation and data sharing to unlock crop variation for nutritional food security (2020)
To quote: “Here, we review generic efforts to standardize the description and management of crop trait data and discuss several issues currently constraining their exchange and comparison, with a focus on knowledge representation using ontologies, and their application to crop‐based dietary nutrition.”
https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/csc2.20092
Semantic Publication of Agricultural Scientific Literature Using Property Graphs (2020)
A pipeline for the generation of scientific literature knowledge graphs in the agriculture domain, consisting of paper RDF generation, including metadata and contents; semantic annotation of the content using AgroPortal; and property graph population by adding domain knowledge from ontologies. Tested on 127 agriculture articles.
https://www.mdpi.com/2076-3417/10/3/861/pdf
Healthy Through Presence or Absence, Nature or Science?: A Framework for Understanding Front-of-Package Food Claims (2019)
The authors study breakfast cereal front-of-packaging marketing claims to determine the validity of “science- and absence-focused claims about ‘removing negatives,’ science- and presence-focused claims about ‘adding positives,’ nature- and absence-focused claims about ‘not adding negatives,’ and nature- and presence-focused claims about ‘not removing positives’. “
https://journals.sagepub.com/doi/10.1177/0743915618824332
FoodKG: A Semantics-Driven Knowledge Graph for Food Recommendation (2019)
A software toolkit that can be used to create a unified food knowledge graph that links various recipe and other food related information.
https://foodkg.github.io
ISO-FOOD ontology: A formal representation of the knowledge within the domain of isotopes for food science (2019)
Focuses on the enumeration of certain stable isotopes and chemical elements within food (organic) compounds, in a new ISO-FOOD ontology.
https://www.sciencedirect.com/science/article/pii/S0308814618319009
The unmapped chemical complexity of our diet (2019)
A position paper exploring the impact and quantity of other chemical compounds besides the more well documented 150+ nutritional components tracked by common food composition databases.
https://www.nature.com/articles/s43016-019-0005-1.pdf
FoodBase corpus: a new resource of annotated food entities (2019)
“A new annotated corpus of food entities, named FoodBase. It was constructed using recipes extracted from Allrecipes, which is currently the largest food-focused social network. The recipes were selected from five categories: ‘Appetizers and Snacks’, ‘Breakfast and Lunch’, ‘Dessert’, ‘Dinner’ and ‘Drinks’. Semantic tags used for annotating food entities were selected from the Hansard corpus.”
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6827550/
ONS: an ontology for a standardized description of interventions and observational studies in nutrition. (2019)
This paper introduces the Ontology for Nutritional Studies (ONS), a Basic Formal Ontology compatible ontology that harmonizing selected pre-existing de facto ontologies with novel health and nutritional terminology classifications in order to describe nutritional studies.
https://www.ncbi.nlm.nih.gov/pubmed/29736190
https://github.com/enpadasi/Ontology-for-Nutritional-Studies
An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content (2019)
A recent ontology development effort focused on the adequate description of nutritional studies with an epidemiology aspect.
https://www.ncbi.nlm.nih.gov/pubmed/31181762h
A rule-based named-entity recognition method for knowledge extraction of evidence-based dietary recommendations (2017)
Introduces drNER, a new named-entity recognition (NER) method that expresses food quantity and units found in text, based on NLP part of speech matching.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0179488
Mapping Food Composition Data from Various Data Sources to a Domain Specific Ontology (2017)
Explores details of how nutrients are referenced in Food composition data (FCD) , specifically EuroFIR and USDA National Nutrient databases, and provides a new Quisper ontology to capture this information.
https://www.researchgate.net/profile/Tome_Eftimov/publication/319102240
Fungi as a source of Food (2017)
A thorough introduction to a wide range of human food Fungi applications.
https://pdfs.semanticscholar.org/dbdd/afa646a170d6e3780fcb42c0799273837520.pdf
Towards Designing an Ontology Encompassing the Environment-agriculture-food-diet-health Knowledge Spectrum for Food System Sustainability and Resilience (2016)
“We seek to build an ontology of food and food systems that encompasses the relevant sustainability issues in their entirety. We have already built an ontology of sustainable sourcing of agricultural raw materials issues and indicators, but aim to expand our ontology to include attributes of resilience, and other issues along the environment-agriculture-food-diet-health knowledge spectrum. Additionally, we aim to create this ontology with the intention of quick usability for the food system decision- maker.”
https://www.academia.edu/63788669/
FOOD: FOod in Open Data (2016)
A recent linked data effort to represent Italian products that have protected names (wine, pasta, fish, oil, etc.).
http://www-kasm.nii.ac.jp/iswc2016/papers/paper_R28_.pdf
Culinary Spice Plants in Dietary Supplement Products and Tested in Clinical Trials
Examines the data harmonization issue of reporting of forms and amounts of culinary spice plants on dietary supplement labels, and how they are referenced in clinical trials.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4785482/
MESCO (MEat Supply Chain Ontology): An ontology for supporting traceability in the meat supply chain (2016)
A data-property focused proposal for a meat product ontology including food processing actors to support food traceability.
https://www.sciencedirect.com/science/article/abs/pii/S095671351630408X
NOVA. The star shines bright (2016)
NOVA is the food classification that categorizes foods according to the extent and
purpose of food processing, rather than in terms of nutrients. It classifies all foods and food products into four clearly distinct and in the authors’ view meaningful groups.
https://archive.wphna.org/wp-content/uploads/2016/01/WN-2016-7-1-3-28-38-Monteiro-Cannon-Levy-et-al-NOVA.pdf
Towards an “Internet of Food”: Food Ontologies for the Internet of Thing (2015)
“In this paper, we review a number of ‘food ontologies’, such as the Food Products Ontology/FOODpedia, Open Food Facts, FoodWiki, FOODS-Diabetes Edition, and AGROVOC multilingual agricultural thesaurus. These food ontologies, with appropriate modifications and together with other relevant non-food ontologies (e.g., about diet-sensitive disease conditions), can […] enable progression from the mere automated identification of food and drinks in our meals to a more useful application whereby we can automatically reason with the identified food and drink items and their details in order to better assist users in making the correct, healthy food and drink choices for their particular health condition, age, body weight/BMI, lifestyle and preferences, etc.”
https://www.academia.edu/64718506
FOODS: A Food-Oriented Ontology-Driven System (2008)
In this paper the authors present the design and development of a counseling system for food or menu planning in a restaurant, clinic/hospital, or at home, the Food-Oriented Ontology-Driven System (FOODS). FOODS comprises (a) a food ontology, (b) an expert system using the ontology, and some knowledge about cooking methods and prices, and (c) a user interface suitable for novices in computers and diets as well as for experts.
https://www.academia.edu/19951183
A multi‐ontology framework to guide agriculture and food towards diet and health (2007)
A visioning paper on formalizing vocabulary around health and nutrition, and linking food nutrition to personal health beyond a framework of physical performance or medical disease.
https://doi.org/10.1002/jsfa.2832
An example of food ontology for diabetes control” (2005)
“This paper describes our experience in the rapid prototyping of a food ontology oriented to the nutritional and health care domain that is used to share knowledge between the different stakeholders involved in the PIPS project.”
https://www.researchgate.net/publication/242305619