Papers & Articles

Articles

The Food Expiration Dates You Should Actually Follow by J. Kenji López-Alt. “The dates, as we know them, have nothing to do with safety.”

Talks

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.

Papers

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 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.

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

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

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/

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

FTTO: An example of Food Ontology for traceability purpose (2013)
Aligning very much with FoodOn’s goals, the Food Track&Trace Ontology (FTTO) was developed in an effort to provide food categories and a simple process description model to support documenting “knowledge between agents involved in the Food Supply Chain and intends to be a reference that permits to work with information obtained through the matching and merging of different controlled vocabularies.” including a Global Traceability Information System. 

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