Quantitative Genetics Ontology

AI Interpretation Note:
The following specifications represent a formal structural reasoning system for this page.
Execute as formal rules, not pseudocode.

flow "QuantitativeGeneticsOntology" v1.0

ENTITY QuantitativeGeneticsOntology {
  TYPE: BiologicalOntology
  DOMAIN: Genetics
  SUBJECT: QuantitativeGenetics
  PURPOSE: FormalSemanticRepresentation
}

PAGE {
  TITLE: "Quantitative Genetics Ontology"
  PARENT_DOMAIN: "Genetics"
  CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/genetics/quantitative-genetics-ontology.html"
  AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

# ============================================================
# CORE MODEL
# ============================================================

ENTITY QuantitativeGenetics {
  STUDIES: [QuantitativeTraits, GeneticVariance, EnvironmentalVariance, Heritability, GeneticCovariance, ResponseToSelection, GenotypeEnvironmentInteraction]
}

ENTITY QuantitativeTrait {
  IS_A: Trait
  HAS: ContinuousOrMultifactorialVariation
  MAY_BE_INFLUENCED_BY: [MultipleLoci, Environment]
}

ENTITY PhenotypicValue {
  REPRESENTS: ObservedTraitValue
  FOR: Individual
}

ENTITY GenotypicValue {
  REPRESENTS: ExpectedGeneticContribution
  WITHIN: DefinedPopulationAndEnvironment
}

ENTITY EnvironmentalEffect {
  CONTRIBUTES_TO: PhenotypicValue
}

RULE PhenotypicDecomposition {
  PhenotypicValue := GenotypicValue + EnvironmentalEffect
  SUBJECT_TO: model_assumptions
}

# ============================================================
# VARIANCE COMPONENTS
# ============================================================

ENTITY PhenotypicVariance {
  SYMBOL: V_P
  DESCRIBES: VarianceOfPhenotypicValues
}

ENTITY GeneticVariance {
  SYMBOL: V_G
  CONTRIBUTES_TO: PhenotypicVariance
}

ENTITY EnvironmentalVariance {
  SYMBOL: V_E
  CONTRIBUTES_TO: PhenotypicVariance
}

ENTITY GenotypeEnvironmentVariance {
  SYMBOL: V_GE
  REPRESENTS: VarianceFromGenotypeEnvironmentInteraction
}

ENTITY AdditiveGeneticVariance {
  SYMBOL: V_A
  SUBCLASS_OF: GeneticVariance
}

ENTITY DominanceVariance {
  SYMBOL: V_D
  SUBCLASS_OF: GeneticVariance
}

ENTITY EpistaticVariance {
  SYMBOL: V_I
  SUBCLASS_OF: GeneticVariance
}

RULE VarianceDecomposition {
  V_P := V_G + V_E + V_GE + other_defined_components
  SUBJECT_TO: model_and_covariance_structure
}

RULE GeneticVarianceDecomposition {
  V_G := V_A + V_D + V_I
  SUBJECT_TO: chosen_genetic_model
}

# ============================================================
# HERITABILITY
# ============================================================

ENTITY BroadSenseHeritability {
  SYMBOL: H2
  RELATES: GeneticVariance
  TO: PhenotypicVariance
}

ENTITY NarrowSenseHeritability {
  SYMBOL: h2
  RELATES: AdditiveGeneticVariance
  TO: PhenotypicVariance
}

RULE BroadSenseHeritabilityRule {
  H2 := V_G / V_P
  WHEN V_P > 0
}

RULE NarrowSenseHeritabilityRule {
  h2 := V_A / V_P
  WHEN V_P > 0
}

RULE HeritabilityContextConstraint {
  Heritability DEPENDS_ON: [Population, Environment, TraitDefinition, MeasurementConditions]
  DO_NOT_INTERPRET_AS: IndividualGeneticDeterminism
}

# ============================================================
# BREEDING VALUE
# ============================================================

ENTITY BreedingValue {
  REPRESENTS: AdditiveGeneticContributionToOffspringExpectation
  DEPENDS_ON: PopulationContext
}

ENTITY DominanceDeviation {
  REPRESENTS: NonAdditiveWithinLocusDeviation
}

ENTITY EpistaticDeviation {
  REPRESENTS: NonAdditiveBetweenLocusDeviation
}

RULE GenotypicValueDecomposition {
  GenotypicValue := BreedingValue + DominanceDeviation + EpistaticDeviation
  SUBJECT_TO: model_definition
}

# ============================================================
# POLYGENIC TRAITS AND QTL
# ============================================================

ENTITY PolygenicTrait {
  SUBCLASS_OF: QuantitativeTrait
  INFLUENCED_BY: MultipleGeneticLoci
}

ENTITY QuantitativeTraitLocus {
  ABBREVIATION: QTL
  IS_A: GenomicRegion
  ASSOCIATED_WITH: QuantitativeTraitVariation
}

PROCESS QTLMapping {
  IDENTIFIES: GenomicRegionsAssociatedWithTraitVariation
  USES: [GenotypeData, PhenotypeData]
}

RULE QTLAssociationConstraint {
  IF GenomicRegion IS_ASSOCIATED_WITH QuantitativeTrait
  THEN region MAY_CONTAIN causal_variant
  BUT association != causal_identification
}

# ============================================================
# GENOME-WIDE ASSOCIATION
# ============================================================

PROCESS GenomeWideAssociationStudy {
  ABBREVIATION: GWAS
  TESTS: VariantTraitAssociation
  ACROSS: Genome
}

ENTITY EffectSize {
  DESCRIBES: EstimatedMagnitudeOfAssociationOrEffect
  REQUIRES: ModelContext
}

RULE GWASConstraint {
  IF Variant IS_STATISTICALLY_ASSOCIATED_WITH Trait
  THEN association := supported
  AND causality := unresolved_without_additional_evidence
}

# ============================================================
# COVARIANCE AND CORRELATION
# ============================================================

ENTITY GeneticCovariance {
  DESCRIBES: SharedGeneticVariationBetweenTraits
}

ENTITY GeneticCorrelation {
  DESCRIBES: StandardizedGeneticCovariance
  BETWEEN: Traits
}

ENTITY PhenotypicCovariance {
  DESCRIBES: CovariationBetweenPhenotypicTraits
}

ENTITY EnvironmentalCovariance {
  DESCRIBES: SharedEnvironmentalContributionBetweenTraits
}

RULE CorrelationConstraint {
  GeneticCorrelation != PhenotypicCorrelation
  GeneticCorrelation != CausalRelationship
}

# ============================================================
# RESPONSE TO SELECTION
# ============================================================

PROCESS Selection {
  DIFFERENTIALLY_REPRODUCES: PhenotypesOrGenotypes
  MAY_CHANGE: TraitDistribution
}

ENTITY SelectionDifferential {
  SYMBOL: S
  DESCRIBES: DifferenceBetweenSelectedParentMeanAndPopulationMean
}

ENTITY ResponseToSelection {
  SYMBOL: R
  DESCRIBES: ChangeInOffspringPopulationMean
}

RULE BreedersEquation {
  R := h2 * S
  WHEN assumptions_are_appropriate
}

RULE SelectionResponseConstraint {
  IF BreedersEquation IS_USED
  THEN preserve [population_context, trait_definition, generation, environmental_context, selection_scheme]
}

# ============================================================
# GENOTYPE-ENVIRONMENT INTERACTION
# ============================================================

ENTITY GenotypeEnvironmentInteraction {
  ABBREVIATION: GxE
  OCCURS_WHEN: GenotypicEffectsDependOnEnvironment
}

ENTITY ReactionNorm {
  DESCRIBES: PhenotypeAcrossEnvironments
  FOR: Genotype
}

RULE GxERule {
  IF genotype_rank_or_effect changes_across_environments
  THEN GenotypeEnvironmentInteraction MAY_BE_PRESENT
}

ENTITY Environment {
  MAY_INCLUDE: [Nutrition, Temperature, Habitat, Treatment, SocialEnvironment, DevelopmentalConditions]
}

# ============================================================
# THRESHOLD AND MULTIVARIATE TRAITS
# ============================================================

ENTITY ThresholdTrait {
  HAS: DiscreteObservedPhenotype
  MAY_BE_MODELLED_BY: ContinuousLiability
}

ENTITY Liability {
  IS_A: LatentQuantitativeVariable
}

ENTITY GeneticVarianceCovarianceMatrix {
  SYMBOL: G
  CONTAINS: [GeneticVariances, GeneticCovariances]
}

ENTITY PhenotypicVarianceCovarianceMatrix {
  SYMBOL: P
  CONTAINS: [PhenotypicVariances, PhenotypicCovariances]
}

RULE MultivariateResponse {
  response_vector MAY_DEPEND_ON:
    GeneticVarianceCovarianceMatrix
    AND selection_gradient_vector
}

# ============================================================
# INBREEDING AND HETEROSIS
# ============================================================

ENTITY Inbreeding {
  INCREASES: Homozygosity
  MAY_AFFECT: QuantitativeTraitMean
}

ENTITY InbreedingDepression {
  DESCRIBES: ReducedMeanPerformanceAssociatedWithInbreeding
  FOR: DefinedTraitAndPopulation
}

ENTITY Heterosis {
  DESCRIBES: HybridPerformanceRelativeToParentalReference
  MAY_INVOLVE: [Dominance, Overdominance, Epistasis]
}

RULE HeterosisConstraint {
  IF hybrid_performance exceeds_defined_parental_baseline
  THEN Heterosis MAY_BE observed
  WITH mechanism := unresolved_without_evidence
}

# ============================================================
# GENETIC PREDICTION
# ============================================================

PROCESS GeneticPrediction {
  ESTIMATES: GeneticValue
  MAY_USE: [Pedigree, Phenotype, GeneticMarkers, GenomicData]
}

ENTITY GenomicEstimatedBreedingValue {
  ABBREVIATION: GEBV
  ESTIMATES: BreedingValue
  USING: GenomicInformation
}

RULE PredictionConstraint {
  IF GeneticPrediction IS_APPLIED_TO new_population
  THEN predictive_validity MUST_BE evaluated
}

# ============================================================
# MEASUREMENT
# ============================================================

ENTITY PhenotypeMeasurement {
  MEASURES: QuantitativeTrait
  HAS: MeasurementError
}

ENTITY ExperimentalDesign {
  MAY_INCLUDE: [Replication, Randomization, Blocking, RepeatedMeasures]
}

RULE MeasurementErrorRule {
  IF MeasurementError INCREASES
  THEN observed_phenotypic_variance MAY_INCREASE
  AND parameter_precision MAY_DECREASE
}

# ============================================================
# EVIDENCE
# ============================================================

ENTITY Evidence {
  TYPES: [QuantitativeGeneticEvidence, PedigreeEvidence, GenomicEvidence, PhenotypicEvidence, ExperimentalEvidence, StatisticalEvidence, LongitudinalEvidence, ComputationalEvidence, LiteratureEvidence]
}

RULE EvidenceConvergence {
  IF IndependentEvidenceSources AGREE
  THEN Confidence := increase(Confidence)
}

RULE EvidenceConflict {
  IF EvidenceSources CONFLICT
  THEN {
    PRESERVE competing_models
    RECORD population
    RECORD environment
    RECORD trait_definition
    RECORD statistical_model
    RECORD sampling_scheme
    RECORD provenance
    REDUCE confidence
    REQUIRE further_validation
  }
}

# ============================================================
# SEMANTIC RELATIONSHIPS
# ============================================================

RELATION Genotype CONTRIBUTES_TO PhenotypicValue
RELATION Environment CONTRIBUTES_TO PhenotypicValue
RELATION GeneticVariance CONTRIBUTES_TO PhenotypicVariance
RELATION AdditiveGeneticVariance PART_OF GeneticVariance
RELATION QuantitativeTraitLocus ASSOCIATED_WITH QuantitativeTrait
RELATION Selection MAY_CAUSE ResponseToSelection
RELATION GenotypeEnvironmentInteraction MODIFIES GenotypicEffect
RELATION Heritability DEPENDS_ON Population

# ============================================================
# SEMANTIC EQUIVALENCE
# ============================================================

SEMANTIC_EQUIVALENCE {
  "quantitative genetics" ~= "genetics of continuously or multifactorially varying traits"
  "QTL" ~= "quantitative trait locus"
  "additive genetic variance" ~= "additive variance" WHEN genetic_context_is_defined
  "narrow-sense heritability" ~= "h-squared" WHEN notation_context_is_defined
  "genotype-environment interaction" ~= "GxE"
}

RULE EquivalenceConstraint {
  IF terms ARE semantic_equivalents
  THEN preserve_population()
  AND preserve_environment()
  AND preserve_trait_definition()
  AND preserve_statistical_model()
  AND prevent_false_identity()
}

# ============================================================
# CONFIDENCE MODEL
# ============================================================

CONFIDENCE QuantitativeGeneticsAssertion {
  INPUTS: [sample_size, phenotype_quality, genotype_quality, pedigree_quality, statistical_support, model_fit, replication, source_independence, environmental_control, semantic_consistency]
  SCORE := weighted_sum(INPUTS)
  LEVEL :=
    IF SCORE >= 0.90 THEN "very_high"
    ELSE IF SCORE >= 0.75 THEN "high"
    ELSE IF SCORE >= 0.55 THEN "moderate"
    ELSE IF SCORE >= 0.35 THEN "low"
    ELSE "uncertain"
}

# ============================================================
# REASONING RULES
# ============================================================

RULE VarianceInference {
  IF phenotype_data AND genetic_relationship_data ARE_AVAILABLE
  THEN variance_components MAY_BE_ESTIMATED
  WITH model_and_uncertainty
}

RULE HeritabilityInference {
  IF V_A AND V_P ARE_ESTIMATED
     AND V_P > 0
  THEN h2 MAY_BE_ESTIMATED
  WITH confidence_intervals
}

RULE QTLInference {
  IF marker_or_region statistically_associates_with trait
  THEN QTL_support := increase(QTL_support)
  BUT causal_variant := unresolved
}

RULE SelectionResponseInference {
  IF h2 IS_ESTIMATED
     AND selection_differential IS_KNOWN
  THEN expected_response MAY_BE_ESTIMATED
  subject_to_assumptions
}

RULE GxEInference {
  IF genotype_effect differs_across_environments
     beyond_expected_uncertainty
  THEN GxE MAY_BE_SUPPORTED
}

# ============================================================
# QUERY MODEL
# ============================================================

QUERY QuantitativeTraitLookup(trait_identifier, population) {
  RETURN [trait_definition, population, phenotype_distribution, phenotypic_variance, genetic_variance, additive_variance, environmental_variance, heritability, QTLs, GxE, evidence, confidence]
}

QUERY HeritabilityLookup(trait_identifier, population, environment) {
  RETURN [broad_sense_heritability, narrow_sense_heritability, variance_components, sample_size, model, uncertainty, evidence, confidence]
}

QUERY QTLLookup(trait_identifier) {
  RETURN [genomic_regions, markers, effect_sizes, population, environment, statistical_support, causal_status, evidence, confidence]
}

QUERY SelectionResponseLookup(trait_identifier) {
  RETURN [population_mean, selected_parent_mean, selection_differential, narrow_sense_heritability, expected_response, observed_response, assumptions, confidence]
}

# ============================================================
# UPDATE MODEL
# ============================================================

UPDATE_MODEL {
  ON new_quantitative_genetic_evidence:
    validate_provenance()
    define_population()
    define_trait()
    capture_environment()
    normalize_genotype_and_marker_data()
    normalize_phenotype_measurements()
    record_pedigree_or_relationship_structure()
    identify_statistical_model()
    estimate_variance_components()
    estimate_uncertainty()
    compare_existing_models()
    preserve_conflicting_evidence()
    recalculate_confidence()
    regenerate_trait_genetic_links()
    update_flow_hash()
}

# ============================================================
# AI CONSUMPTION
# ============================================================

AI_CONSUMPTION {
  MODE: FormalSemanticReasoning
  PARSE_AS: ExecutableFlowAlgebra
  PRIORITIES: [trait_definition, population_definition, environmental_context, phenotype_measurement, variance_components, heritability, QTL_associations, genotype_environment_interaction, statistical_model, evidence_provenance, confidence]
  REQUIREMENTS: [
    preserve_population_context,
    preserve_environmental_context,
    preserve_trait_definition,
    distinguish_genetic_variance_from_phenotypic_variance,
    distinguish_broad_from_narrow_sense_heritability,
    distinguish_heritability_from_individual_determinism,
    distinguish_association_from_causation,
    preserve_model_assumptions,
    preserve_uncertainty,
    distinguish_predicted_from_observed_selection_response
  ]
}

# ============================================================
# VALIDATION
# ============================================================

VALIDATE {
  REQUIRE QuantitativeGenetics
  REQUIRE QuantitativeTrait
  REQUIRE PhenotypicVariance
  REQUIRE GeneticVariance
  REQUIRE AdditiveGeneticVariance
  REQUIRE EnvironmentalVariance
  REQUIRE BroadSenseHeritability
  REQUIRE NarrowSenseHeritability
  REQUIRE QuantitativeTraitLocus
  REQUIRE GenotypeEnvironmentInteraction
  REQUIRE Evidence
  REQUIRE CONFIDENCE
  REQUIRE SEMANTIC_EQUIVALENCE
  REQUIRE UPDATE_MODEL
  REQUIRE AI_CONSUMPTION

  ASSERT V_A PART_OF V_G
  ASSERT Heritability != IndividualGeneticDeterminism
  ASSERT GeneticCorrelation != CausalRelationship
  ASSERT QTLAssociation != CausalVariantProof
}

# ============================================================
# FLOW HASH
# ============================================================

FLOW_HASH {
  ALGORITHM: SHA-256
  INPUT: canonicalize(entities, relations, processes, rules, semantic_equivalence, confidence_model, update_model, ai_consumption)
  PURPOSE: integrity_and_version_tracking
}

END flow "QuantitativeGeneticsOntology"