Ontology Design Guide

An ontology is a formal, explicit specification of a shared
conceptualization. In practical terms, it defines:

  - Classes: Categories of things (e.g., Gene, Disease, Drug)
  - Properties: Relationships between things (e.g., causes, treats)
  - Individuals: Specific instances (e.g., TP53, Breast Cancer)
  - Axioms: Rules and constraints (e.g., every Drug has exactly
    one molecular formula)

Purpose in research:
  - Standardize terminology across research groups
  - Enable data integration from heterogeneous sources
  - Support automated reasoning and inference
  - Facilitate knowledge discovery through graph queries
  - Provide machine-readable domain models

Taxonomy:       Hierarchical classification (is-a relationships only)
                Example: Animal > Mammal > Primate > Human

Ontology:       Formal model with classes, properties, and axioms
                Supports reasoning (e.g., if X treats Y and Y is-a Disease,
                then X is a DrugCandidate)

Knowledge Graph: An ontology populated with instance data
                 Millions of triples: (subject, predicate, object)
                 Examples: Wikidata, DBpedia, Google Knowledge Graph

def ontology_design_process(domain: str) -> dict:
    """
    Steps for designing a domain ontology.

    Args:
        domain: The research domain to model
    """
    return {
        "step_1_scope": {
            "description": "Define scope and competency questions",
            "questions": [
                "What domain does the ontology cover?",
                "What questions should the ontology be able to answer?",
                "Who will use it and for what purpose?"
            ],
            "example": (
                "Domain: Drug-disease interactions. "
                "Competency question: 'What drugs target proteins "
                "associated with Alzheimer disease?'"
            )
        },
        "step_2_reuse": {
            "description": "Search for existing ontologies to reuse",
            "resources": [
                "BioPortal (bioportal.bioontology.org) -- biomedical ontologies",
                "Linked Open Vocabularies (lov.linkeddata.es) -- general",
                "OBO Foundry (obofoundry.org) -- life sciences",
                "Schema.org -- web-scale vocabulary"
            ]
        },
        "step_3_enumerate": {
            "description": "List key terms, concepts, and relationships",
            "method": "Brainstorm with domain experts; review literature"
        },
        "step_4_model": {
            "description": "Define class hierarchy and properties",
            "tools": ["Protege", "WebVOWL", "TopBraid Composer"]
        },
        "step_5_formalize": {
            "description": "Encode in OWL/RDF with axioms and constraints"
        },
        "step_6_validate": {
            "description": "Test against competency questions and real data",
            "methods": ["SPARQL queries", "Reasoner (HermiT, Pellet)", "Unit tests"]
        },
        "step_7_publish": {
            "description": "Publish with persistent URI and documentation",
            "best_practice": "Use w3id.org or purl.org for persistent identifiers"
        }
    }

RDF (Resource Description Framework) represents knowledge as triples:

  (Subject, Predicate, Object)

Examples:
  (:Aspirin, :treats, :Headache)
  (:TP53, rdf:type, :Gene)
  (:TP53, :associatedWith, :BreastCancer)
  (:Aspirin, :hasChemicalFormula, "C9H8O4")

Serialization formats:
  - Turtle (.ttl): Human-readable, most common for authoring
  - JSON-LD (.jsonld): Web-friendly, API-compatible
  - RDF/XML (.rdf): Verbose, legacy format
  - N-Triples (.nt): Simple, good for large datasets

@prefix : <http://example.org/research#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .

# Classes
:Gene a owl:Class ;
    rdfs:label "Gene" ;
    rdfs:comment "A unit of heredity in a living organism." .

:Disease a owl:Class ;
    rdfs:label "Disease" .

:Drug a owl:Class ;
    rdfs:label "Drug" .

# Properties
:associatedWith a owl:ObjectProperty ;
    rdfs:domain :Gene ;
    rdfs:range :Disease .

:treats a owl:ObjectProperty ;
    rdfs:domain :Drug ;
    rdfs:range :Disease .

# Individuals
:TP53 a :Gene ;
    rdfs:label "TP53" ;
    :associatedWith :BreastCancer .

:BreastCancer a :Disease ;
    rdfs:label "Breast Cancer" .

# Find all genes associated with Breast Cancer
SELECT ?gene ?geneLabel
WHERE {
  ?gene a :Gene .
  ?gene :associatedWith :BreastCancer .
  ?gene rdfs:label ?geneLabel .
}

# Find drugs that treat diseases associated with gene TP53
SELECT ?drug ?disease
WHERE {
  :TP53 :associatedWith ?disease .
  ?drug :treats ?disease .
}

# Count diseases per gene
SELECT ?gene (COUNT(?disease) AS ?diseaseCount)
WHERE {
  ?gene a :Gene .
  ?gene :associatedWith ?disease .
}
GROUP BY ?gene
ORDER BY DESC(?diseaseCount)