Building the farm to fork digital highway: integrated food ontology development for agricultural, food science and public health domains

This is a virtual conference beginning September 16th, 2020 presented as part of the International Conference on Biomedical Ontologies (ICBO) presence within BOSC 2020 (see https://icbo2020.inf.unibz.it/accepted-workshops/).  We will be having 2 hour virtual conferences, once a week, at 6am PDT, 9am EDT, 3pm CEST, 11pm AEST for each of the sessions outlined below.

• Wednesday, Sept 16: Field to Food Session
• Wednesday, Sept 23: Food in the Body Session
• Wednesday, Sept 30: In the Agency / Organization / Company Session
• Wednesday, Oct 7    : Tools for ontology building, quality metrics, database integration and process analysis.

Previous session abstract and presentation content is now available at: https://github.com/FoodOntology/joint-food-ontology-wg/tree/master/presentation .

A video of each workshop is now available on the Biomedical Ontology World YouTube playlist called “Integrated Food Ontology Workshop“.

Note: The main ICBO conference committee has stated that all main-conference paper submissions can be presented in person a year later in Bolzano, in addition to whatever virtual conference participation that may occur this year. Our own IFOW workshop will continue regardless of paper submissions to the main conference.  IFOW itself will not itself be producing conference proceedings-related publications.

We are encouraging people to consider this an opportunity to meet and connect with peers from interrelated disciplines, and to discover the full breadth of ontology research occurring in the food domain.

Abstract submission deadline CLOSED: June 30, 2020 (extended to July 7, 2020!)

Abstract notice of acceptance SENT: July 27, 2020 (July 30, 2020)

Introduction

Controlled vocabulary standardization efforts covering agricultural and food domains are evolving since their inception decades ago thanks to the mandates and continued support of institutional caretakers. Popular examples are FoodEx2, the European Food Safety Authority (EFSA) food classification and description system, the Global Language of Business GS1 product categorization scheme, the EUROFIR promoted LanguaL food composition thesaurus, the UN Food and Agriculture Organization’s AGROVOC SKOS-based vocabulary, and its support of the International Network of Food Data Systems (INFOODS) vocabulary for food nutrition testing. These vocabularies are used in a growing interconnected food database landscape but suffer from format issues like textual or spreadsheet formats, unresolvable identifiers, and inconsistent category semantics.

Ontologies are new entrants into the food domain, bringing a wave of Semantic Web technology and philosophy to bear on the issue of data sharing and modelling of food-related activity and research which are becoming critical in the face of rapid change to our environment and anthroposphere. Examples range from BBC’s Food Ontology, driving its culinary media universe, to recently published research laboratory initiated ontologies like OBOFoundry members FoodOn, the Food Biomarker Ontology (FOBI), and the Ontology for Nutritional Studies (ONS), and related ontologies like the Medical Action Ontology (MAxO) and the Environmental Conditions, Treatments and Exposures ontology (ECTO) that are under development. Underpinning these mid-level, model-focused ontologies are environmental, chemical, biological, anatomical, disease and phenotype ontologies.

Academic, agricultural and public health agencies are considering the benefits and complexities of adopting ontology in their research and data management and reporting infrastructure. How can ontologies interface to legacy datasets and online databases described by existing vocabularies? What vocabulary, tool ecosystem and data models are needed to correlate agricultural treatments, nutritional data, eating patterns, biomarkers, pathogens, and phytochemical levels with disease and health phenotypes? This workshop seeks to define the coverage of the different ecological, agricultural, nutritional, dietary, public health, one health surveillance, food security, and trade domains that food-related ontologies are modelling, and the use of data translation tools for bringing legacy data into the ontology fold.

Workshop will have 2 hour sessions split into presentations of relevant ontologies / projects and their scope in the first hour, in 10-15 minute slots + 5 for a few questions, followed by 1 hour discussion and a break as schedule allows.

Wednesday, Sept 16: Field to Food: Food component modelling

This session follows the ontological description of food from its inception in wild and agricultural contexts up to the point of food product nomenclature. How should agricultural field studies be modelled, and can this adapt to commercial farm data collection? One of the challenges with agricultural field modelling is having to rely on estimated (or subjective) vs actual data since proper measurements occur in limited circumstances. A second challenge is collecting data from farms with heterogeneous practices in large, remote areas in a way respecting privacy. Use of agricultural chemicals and their potential inclusion in food products must also be considered. Another challenge for research, food traceability and correct product labelling is that product vocabulary varies by region, language and industry, a situation which ontologies should help to alleviate. Another formidable challenge is the ontology modelling of food biochemistry of plants and animal products, including their biotransformation from fungi, and bacteria, and how they are taken in the body through dietary eating patterns. Modelling of bioactive food related compounds requires a schema for nutrients, additives, and contaminants, as well as diet terms and regimens.

Chair: Robert Warren

Accepted presentations:

• FoodOn Evolution in the Food Ontology Ecosystem (Damion Dooley, Emma Griffiths, Rhiannon Cameron, Gurinder Gosal, Tarini Naravane, Ramona L. Walls, Pier Buttigieg, William Hsiao)
• The Crop Dietary Nutrition Ontology (CDNO): aligning the domains of production and consumption (Liliana Andrés-Hernández, Razlin Azman Halimi, Abdul Baten, Kai Blumberg, Damion Dooley , Ben Liu, Ramil Mauleon, Ramona Walls, Graham J. King)
• The Plant Trait Ontology Links Wheat Traits for Crop Improvement and Genomics (Laurel Cooper, Marie-Angélique Laporte, Justin Elser, Victoria Carollo Blake, Taner Sen, Chris Mungall, Elizabeth Arnaud and Pankaj Jaiswal)
• The Agronomy Ontology (AgrO): A semantic layer to standardize agronomic data in farming systems research and development (Céline Aubert, Marie-Angélique Laporte, Elizabeth Arnaud and Medha Devare)

Wednesday, Sept 23: Food in the Body: Modelling metabolic transformation of food and exposure to food-borne toxicants

Can we model the complex web of metabolic transformations leading from food components to beneficial bioactives for health maintenance or improvement? This session welcomes contributions dealing with ontology modeling of bioactive molecules derived and/or modified from food components by human metabolism, by gut microbiome metabolism, and their synergy. We include xenobiotic metabolism and exposure through food as well. Finally, a major component of human diet is in fermented foods, so modelling the role of microbial fermentations from pure culture or microbial communities and the metabolic interactions between the components of the microbial web is important. Food allergen and other linkages between food components and disease phenotypes are also needed.

Chair: Damion Dooley

Accepted presentations:

• Representing Foods Potentially Involved in Food-Drug Interactions using FoodOn (FIDEO) (Georgeta Bordea, Thierry Hamon, Fleur Mougin)
• FOBI: An ontology to represent food intake data and associate it with metabolomic data (Pol Castellano-Escuder, Raúl González-Domínguez, David S. Wishart, Cristina Andrés-Lacueva and Alex Sánchez-Pla)
• The Ontology for Nutritional Studies (ONS) and its future directions (Francesco Vitali, Agnese Gori, Paola Zinno, Emily Schifano, Chiara Devirgiliis and Duccio Cavalieri)
• Ontology for Nutritional Epidemiology (ONE) (Chen Yang, Carl Lachat)
• Sensory experiment on dietary intervention for health (Tarini Naravane and Ekta Parpia Naravane)

Wednesday, Sept 30: In the agency: Ontology ecosystem to support research and operational adoption

The promise that ontology will fix data interoperability carries possible failure points along a two-directional dependency chain that has term curation at one end, then dataset curation by trained agency staff according to selected vocabulary and design patterns, then the provision of that data to federated querying or consolidated databases, and lastly, users tasked with querying and learning about what are potentially very complex data structures. Are success stories accumulating as ontology identifiers surface within a diversity of databases?

Chair: Emma Griffiths

Accepted presentations:

• You Can’t Grow Ontologies from Bad Soil (Robert Warren, Jessica Singer)
• USDA ARS FoodData Central Ontology Integration (Kyle A. McKillop, Damion M. Dooley, Tarini Naravane, James M. Harnly, John Finley, Naomi K. Fukagawa)
• Inclusion of Dietary Supplements as a Subcategory of Foods in Food Ontology Systems (Leila Saldanha, Johanna T Dwyer, Richard Bailen)
• FDA Development of a MIxS (Minimum Information about any (x) Sequence) Food Environmental Metadata Standard (Christopher J. Grim, Amanda M. Windsor, Brandon Kocurek, Susan R. Leonard, Taylor K. S. Richter, Gopal Gopinath, Maria Balkey, Padmini Ramachandran, Andrea Ottesen, Karen Jarvis and Ruth Timme)
• Health Surveillance Ontology: supporting semantic interoperability in One-Health (Fernanda Dorea, Estibaliz Lopez de Abechuco Garrido, Nazareno Scaccia and Matthias Filter)

Wednesday, October 7: Tools for ontology building, quality metrics, database integration and process analysis

Given the complexity of integrating ontology into databases and applications, and the aspiration to provide high-quality internally coherent vocabulary, there is a pressing need to develop quality control and content-matching tools, and demonstrate the benefit of applications that are fully driven by ontology.

Chair: Hande Kucuk McGinty

Accepted presentations:

• Tool Support for Ontology Design and Quality Assurance (Ian Horrocks, Jiaoyan Chen and Jaehun Lee)
• A new alignment method based on FoodOn as pivot ontology to integrate nutritional legacy data sources (Patrice Buche, Julien Cufi, Stéphane Dervaux, Juliette Dibie, Liliana Ibanescu, Alrick Oudot, Magalie Weber)
• Food transformation process description using PO2 and FoodOn (Patrice Buche, Julien Cu, Stephane Dervaux, Juliette Dibie, Liliana Ibanescu, Alrick Oudot, Magalie Weber)
• LexMapr – A rule-based biomedical text-mining tool for entity recognition and ontology-driven classification (Gurinder Gosal, Emma Griffiths, Damion Dooley, Ivan Gill, William Hsiao)
• You are what you eat:an analytical approach to build a food ontology for elderly. (Usashi Chatterjee, Fernando Loizides)

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Organizing committee

Leigh Carmody	Robinson Lab / Jackson Laboratory
Melissa Haendel	Translational and Integrative Sciences Lab, Oregon State University
Lauren Chan	Oregon State University
Lynn Schriml	University of Maryland
Duccio Cavalieri	Department of Biology – University of Florence
Tarini Naravane	University of California, Davis
Damion Dooley	Hsiao Lab, University of British Columbia
Robert Warren	Myra Analytics
Jessica Singer	Myra Analytics