ICBO Sept 16, 2020 Integrated food ontology workshop

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 JOWO 2020 (see https://icbo2020.inf.unibz.it/accepted-workshops/).  We will be having 2 hour virtual conferences, once a week, for each of the sessions outlined below.

Note: In light of the coronavirus crisis, the conference is being held virtually, with a commitment by ICBO 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. More details on that will be available in June 2020.  Our own IFOW workshop will continue regardless of paper submissions to the main conference, in other words you may submit your work to us for presentation this fall, in addition to participating in ICBO and its conference proceedings.  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.

Submit your paper/presentation at https://easychair.org/cfp/IFOW-2020

Abstract submission deadline: June 30, 2020

Abstract notice of acceptance: July 27, 2020


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.

Session: In the food: Food component modelling

Modelling biochemical food components, and how they are taken in the body through dietary eating patterns. Food biochemistry of plants and animal products, including their biotransformation from fungi, and bacteria. Modelling of bioactive food related compounds including nutrients, additives, and contaminants, as well as diet terms and regimens. Food allergen and other linkages between food components and disease phenotypes. Finally modeling the role of microbial fermentations from pure culture or microbial communities and the metabolic interactions between the components of the microbial web will be a task.

Session: 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.

Session: In the field: Agricultural production modelling

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. Finally, vocabularies for product vary by region, language and industry making vocabularies a necessity for research, food traceability and correct product labelling.

Session: 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?

In addition to discussion-oriented presentation in the above tracks, we welcome other tangible food experience workshop ideas. The following is an example.

Request for Proposals for Tasting Experience

Long term benefits of diet are dependent on a person’s ability to stick to a diet. Can consumers tune their individual palatability to foods that offer more nutrition? Can food science offer more palatable foods that don’t suffer nutrition loss associated with processed foods?  We welcome proposals that demonstrate this on the workshop audience with foods that are easily sampled on site. It could be a blind taste test! Experiential variables could include sensory response (comparing products with known nutritional profiles/health benefits vs products without that emphasis) and time of experience (relate foods to physiology needs based on time of day).

Organizing committee

Leigh Carmody Robinson Lab / Jackson Laboratory
Melissa HaendelTranslational and Integrative Sciences Lab,
Oregon State University
Lauren ChanOregon State University
Lynn SchrimlUniversity of Maryland
Duccio CavalieriDepartment of Biology – University of Florence
Tarini NaravaneUniversity of California, Davis
Damion DooleyHsiao Lab, University of British Columbia
Robert WarrenAnnex Agriculture Inc.
Jessica SingerAnnex Agriculture Inc.