Ontomatica Expertise

Table of Contents

Overview

Ontomatica integrates knowledge and informatics about foods, agricultural commodities, agrochemicals and pharmaceuticals. Knowledge and informatics are documented as Ontologies, from which production systems are generated. Scope of Ontomatica expertise is demonstrated in more than twenty (20) production systems. Twelve (12) systems are presented below.

Chemical, Food, Therapeutic, Clinical and Research Databases

ChEFS - Chemical Entities of Food Significance

50,000+ chemicals organized by Facets

• Bioactive Capabilities of Specific Chemicals
• Biological Effects of Specific Chemicals
• Chemical Capabilities
• Chemical Category
• Food Nutrient and Dietary Chemicals
• Food Pesticide Chemicals with Regulated Residues on Food Commodities
• Industrial Uses
• Name of Biological Source of Chemical
• Part of Biological Source of Chemical

Example:ChEFS Significance:Precise chemical classification and relationships with Authorities and uses.

ChEMATIC - Chemical Entities with Medical Applications, Therapeutic Indications and Consequences

300,000+ substances organized by Facets

• Amino Acids, Peptides, and Proteins
• Biological Factors
• Carbohydrates
• Chemical Actions and Uses
• Complex Mixtures
• Enzymes and Coenzymes
• Heterocyclic Compounds
• Hormones, Hormone Substitutes, and Hormone Antagonists
• Inorganic Chemicals
• Lipids
• Macromolecular Substances
• Nucleic Acids, Nucleotides, and Nucleosides
• Organic Chemicals
• Pharmaceutical Preparations
• Polycyclic Compounds

and their relationship with

• Anatomy
• Diseases and Disorders (26 classes)
• Human Genes
• Organisms

Example:ChEMATIC Significance:Precise substance classification and relationships with human disorders, human genes and interactions between substances and genes.

Dietary Data Reference

Food items organized by these Facets

• Adjunct Characteristics
• Consumer Group / Dietary Use /Label Claim
• Contact Surface
• Container or Wrapping
• Cooking Method
• Extent of Heat Treatment
• Geographic Places and Regions
• Identifying Substance
• Packing Medium
• Part of Substance
• Physical State, Shape or Form
• Preservation Method
• Regulatory Category
• Substances Included
• Treatment Applied

Example:Dietary Data Reference Significance:Foods and their relationships with dietary chemicals, food preparation techniques, food packaging substances and food label claims.

USDA National Nutrient Database for Standard Reference

Standard Reference items organized by these Facets

• Food Source
• Index to Food Descriptions (A - Z)
• Product Type
• Substances Included

Example:USDA National Nutrient Database for Standard Reference Significance:USDA SR implemented in Facet navigation architecture.

Specialty Foods and GS1

Same structure as Dietary Data Reference but with different items

Example:Specialty Foods and GS1

Basic Food Data Kit

Food commodities organized by these Facets

• Commodities by Crop Group
• Commodities by Food Group
• Food Source
• Index to Food Commodity Names (A - Z)
• Part of Food Source
• Scientific Name

Example:Food Data Kit - Basic Significance:Food commodities and relationships with UN FAO, USDA and US EPA regulatory and identity terms.

USDA Food and Nutrient Database for Dietary Studies

Food and meal items organized by these Facets

• Constituents by Crop Group
• Constituents by Food Group
• Food Descriptions and Constituents
• Index to Food Descriptions (1 - 3; A - Z)

Example:USDA Food and Nutrient Database for Dietary Studies - with EPA FCID Significance:Unique implementation of USDA FNDDS foods and meals and their relationships with UN FAO, USDA and US EPA regulatory and identity terms.

Reference Library (based on National Agricultural Library Thesaurus)

Agriculture-related items organized by these Facets

• Animal Science and Animal Products
• Biological Sciences
• Breeding and Genetic Improvement
• Calendar Year
• Economics, Business and Industry
• Farms and Farming Systems
• Food and Human Nutrition
• Forest Science and Forest Products
• Geographical Locations
• Government, Law and Regulations
• Health and Pathology
• Insects and Entomology
• Natural Resources, Earth and Environmental Sciences
• Physical and Chemical Sciences
• Plant Science and Plant Products
• Reference Types
• Research, Technology and Engineering
• Rural and Agricultural Sociology
• Taxa - Algae
• Taxa - Animalia
• Taxa - Archaea, Cyanobacteria and Bacteria
• Taxa - Fungi, Yeasts, Molds and Mildews
• Taxa - Plantae
• Taxa - Viruses and Viroids
• Time Periods

Example:Reference Library - based on National Agricultural Library Thesaurus (NALT) Significance:Unique implementation of USDA NALT and relationships with published articles about food and agriculture science.

Dietary Supplements and FDA SPL

• Dietary supplement items organized by these Facets
• Additive Treatments
• Contact Surface
• Container or Wrapping
• Dietary Supplement Products
• Dosage Form
• Label Claims
• Manufacturing Procedures
• Nutrients
• Part of Source
• Preservation Methods
• Product Documentation
• Region of Origin
• Sensory Terms
• Source of Base Ingredient
• Supplement Treatments
• Treatments Applied

Example:Dietary Supplements and FDA SPL Significance:Supplements in a Facet navigation architecture with a structure that aligns with US FDA Structured Product Label terms.

Homeopathic Remedies

Homeopathic remedy items organized by these Facets

• Animal Science and Animal Products
• Biological Sciences
• Economics, Business and Industry
• Health and Pathology
• Physical and Chemical Sciences
• Plant Science and Plant Products
• Research, Technology and Engineering
• Scientific Classification
• Sociology

Example:Homeopathic remedies and FDA SPL Significance:Similar to dietary supplements but where Items are homeopathic remedies.

Glucosinolate Content in Brassica

Phytochemical items organized by these Facets

• Adjunct Characteristics
• Affiliations
• Anatomical Part
• Biological Source
• Data Acquisition Type
• Data Reference Type
• Extent of Heat Treatment
• Genetic Characteristics
• Geographic Regions
• Growing Conditions
• Matrix Values
• Maturity Period
• Measurement Units
• Method Indicators
• Method Type
• Nitrogen Components
• Organosulfur Compounds
• Physical State, Shape or Form
• Product Type
• Review Status
• Time Periods
• Treatment Applied
• Years

Example:Glucosinolate Content in Brassica Significance:Unique implementation of food and chemistry research integrates data from scientific analysis with a Facet navigation architecture.

Plants

Plant taxonomy database using biological classification.

• Kingdom
• Division
• Class
• Order
• Family
• Subfamily
• Tribe
• Genus
• Species

Example:Plants Significance:Uses USDA Germplasm Resources Information Network (GRIN).

Related Projects

Research Data Depository

Ontomatica is building a data depository where results from scientific research about foods, agriculture and related compounds and substances will be stored.

Glucosinolate Content in Brassica is a prototype.

Depository components are summarized in use case below.

• Isothiocyanates occur widely in nature and are of interest in food science and medicine. Vegetable foods with characteristic flavors due to isothiocyanates include wasabi, horseradish, mustard, radish, Brussels sprouts, watercress, nasturtiums, and capers. These vegetables generate isothiocyanates in different proportions and have unique flavors.
• Isothiocyanates are produced by enzymatic conversion of metabolites called glucosinolates. Sulforaphane is a type of isothiocyanate. It is produced when enzyme thioglucosidase transforms glucoraphanin, a glucosinolate, into sulforaphane upon damage to the plant (such as from chewing), which allows two compounds to mix and react.
• Sulforaphane is a potent inducer of metabolic detoxication, phase 2. Detoxication 2 induction is associated with reduced susceptibility of animals and their cells to toxic and neoplastic effects of carcinogens. Data from several research projects demonstrate that Sulforaphane blocks chemical carcinogenesis.
• Research data about sulforaphane, specific vegetables, detoxication 2 and chemical carcinogenesis will be managed by Ontomatica Depository and accessible to other Researchers.

Food specifications designed for a Food SPL

Structured Product Labeling (SPL) is a document markup standard approved by Health Level Seven (HL7) and adopted by US FDA as a mechanism for exchanging drug product information.

Ontomatica modified US FDA SPL structure as a mechanism for exchanging food product information

• As a baseline, here are lasagna nutrient properties from USDA Standard Reference.
• Here are lasagna nutrient properties in a form consistent with US FDA SPL structure.

Comprehensive Ontologies

Ontomatica work is represented as an ontology and documented in Web Ontology Language (OWL) format. Three examples - Pizza, Wheat and Microbiome - are presented.

Pizza Ontology

An example of a food ontology is Pizza Ontology. As a baseline, here is pizza as implemented in USDA FNDDS.

• Pizza Ontology as implemented in OWL.
• Pizza Ontology as a Graph.
• Pizza Ontology as multiple Graphs for easier reading.

Wheat Ontology

Ontomatica Wheat Ontology has two dimensions: (1) Facets associated with process of growing wheat; (2) Predicates expressing relationships between wheat and Facet Terms.

Figure below summarizes 13 Facet Classes and 13 Predicate Classes that define wheat.

Specific type of wheat (i.e., cultivar) is the Item.

Facets	Predicates relating Facets to Item (wheat)
Plant (weed)	Anatomy and Morphology
Insect	Development
Fungus	Pathology
Bacteria	Action and Usage
Virus	Administration
Animal	Trait
Chemical	Bioactive Property
Soil	Biochemical Pathway
Atmosphere	Breeding and Genetic Improvement
Water	Farming System
Time	Metrology
Geographical Location	Agricultural Economics
Agricultural Machinery	Authority, Law and Regulation

Wheat Ontology is used to represent USDA Objective Description of Wheat as an electronic message.

Microbiome Ontology

Human microbiome is Classes of microbes that participate in process of unlocking dietary plant and animal nutrients.

Microbes include bacteria, archaea and viruses, such as bacteriophages.

Ontomatica Microbiome Ontology implements relationships between food intake; bacteria, archaea and viruses; human anatomy (location of microbe Classes e.g., human gut); and, health outcomes.

Summary

Examples and projects above demonstrate that Ontomatica is the world leader in building information systems delivering knowledge and informatics about foods, agricultural commodities, agrochemicals and pharmaceuticals.