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.