Heredity Ontology

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

flow "HeredityOntology" v1.0

ENTITY HeredityOntology {
  TYPE: BiologicalOntology
  DOMAIN: Genetics
  SUBJECT: Heredity
  PURPOSE: FormalSemanticRepresentation
}

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

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

PROCESS Heredity {
  IS_A: BiologicalInheritanceProcess
  TRANSMITS: GeneticInformation
  FROM: Parent
  TO: Offspring
  ACROSS: Generations
}

ENTITY GeneticInformation {
  STORED_IN: GeneticMaterial
  ORGANIZED_AS: [Genome, Chromosome, Gene]
  TRANSMITTED_BY: Heredity
}

ENTITY Parent {
  CONTRIBUTES: GeneticMaterial
  TO: Offspring
}

ENTITY Offspring {
  RECEIVES: GeneticMaterial
  FROM: ParentOrParents
  HAS: Genotype
}

ENTITY Generation {
  REPRESENTS: ReproductiveStep
  LINKS: ParentGeneration
  TO: OffspringGeneration
}

# ============================================================
# GENETIC MATERIAL
# ============================================================

ENTITY Genome {
  CONTAINS: GeneticInformation
  ORGANIZED_INTO: Chromosome
}

ENTITY Chromosome {
  PART_OF: Genome
  CONTAINS: Gene
  TRANSMITTED_DURING: Reproduction
}

ENTITY Gene {
  IS_A: HereditaryInformationUnit
  LOCATED_AT: GeneticLocus
  MAY_HAVE: Allele
}

ENTITY Allele {
  IS_A: AlternativeStateAtGeneticLocus
  MAY_BE_TRANSMITTED_TO: Offspring
}

ENTITY GeneticLocus {
  IDENTIFIES: PositionOrRegion
  WITHIN: Genome
}

# ============================================================
# GENOTYPE AND PHENOTYPE
# ============================================================

ENTITY Genotype {
  REPRESENTS: GeneticState
  COMPOSED_OF: AllelicStates
  MAY_CONTRIBUTE_TO: Phenotype
}

ENTITY Phenotype {
  REPRESENTS: ObservableOrMeasurableTraitState
  INFLUENCED_BY: [
    Genotype,
    Environment,
    Development,
    EpigeneticState
  ]
}

RULE GenotypePhenotypeConstraint {
  IF Genotype IS_INHERITED
  THEN DO_NOT_ASSUME Phenotype IS_IDENTICAL_TO_PARENT
  BECAUSE phenotype_depends_on_context
}

# ============================================================
# GAMETE FORMATION
# ============================================================

ENTITY Gamete {
  IS_A: ReproductiveCell
  CARRIES: GeneticMaterial
}

PROCESS GameteFormation {
  MAY_USE: Meiosis
  PRODUCES: Gamete
}

PROCESS Meiosis {
  REDUCES: ChromosomeSetNumber
  PRODUCES: HaploidCells
  ENABLES: [Segregation, Recombination]
}

PROCESS Segregation {
  SEPARATES: AllelicCopies
  DURING: GameteFormation
}

RULE AlleleTransmissionRule {
  IF diploid_parent HAS alleles A and a at locus
  THEN gametes MAY_CARRY A OR a
  ACCORDING_TO segregation_and_linkage_context
}

# ============================================================
# FERTILIZATION
# ============================================================

PROCESS Fertilization {
  COMBINES: Gametes
  PRODUCES: Zygote
}

ENTITY Zygote {
  RECEIVES: GeneticMaterial
  FROM: ContributingGametes
  DEVELOPS_INTO: Offspring
}

RULE BiparentalInheritanceRule {
  IF reproduction IS_BIPARENTAL
  THEN offspring_genome derives_from genetic_contributions_of_both_parents
  SUBJECT_TO organellar_and_special_inheritance_patterns
}

# ============================================================
# ASEXUAL HEREDITY
# ============================================================

PROCESS AsexualReproduction {
  PRODUCES: Offspring
  FROM: SingleParent
  MAY_TRANSMIT: NearParentalGenotype
}

RULE AsexualInheritanceRule {
  IF reproduction IS_ASEXUAL
  THEN offspring_genetic_state MAY_CLOSELY_RESEMBLE parent
  EXCEPT_FOR mutation_recombination_or_genomic_change
}

# ============================================================
# MENDELIAN HEREDITY
# ============================================================

ENTITY MendelianInheritance {
  SUBCLASS_OF: HeredityModel
  BASED_ON: [Segregation, IndependentAssortment]
}

ENTITY DominanceRelationship {
  RELATES: Alleles
  WITH_RESPECT_TO: Phenotype
}

RULE MendelianSegregationRule {
  IF locus HAS two_homologous_allelic_copies
  THEN gamete typically_receives one_copy
}

RULE IndependentAssortmentConstraint {
  IF loci ARE_LINKED
  THEN DO_NOT_ASSUME complete_independent_assortment
}

# ============================================================
# AUTOSOMAL INHERITANCE
# ============================================================

ENTITY AutosomalInheritance {
  SUBCLASS_OF: HeredityPattern
  LOCUS_ON: Autosome
}

CLASS AutosomalDominantInheritance {
  SUBCLASS_OF: AutosomalInheritance
}

CLASS AutosomalRecessiveInheritance {
  SUBCLASS_OF: AutosomalInheritance
}

# ============================================================
# SEX-LINKED INHERITANCE
# ============================================================

ENTITY SexLinkedInheritance {
  SUBCLASS_OF: HeredityPattern
  LOCUS_ON: SexChromosome
}

CLASS XLinkedInheritance {
  SUBCLASS_OF: SexLinkedInheritance
  LOCUS_ON: XChromosome
}

CLASS YLinkedInheritance {
  SUBCLASS_OF: SexLinkedInheritance
  LOCUS_ON: YChromosome
}

RULE SexLinkedRule {
  IF inherited_locus IS_ON SexChromosome
  THEN transmission_probabilities MUST_ACCOUNT_FOR sex_chromosome_complement
}

# ============================================================
# MITOCHONDRIAL AND CYTOPLASMIC INHERITANCE
# ============================================================

ENTITY CytoplasmicInheritance {
  SUBCLASS_OF: HeredityPattern
  INVOLVES: CytoplasmicGeneticMaterial
}

ENTITY MitochondrialInheritance {
  SUBCLASS_OF: CytoplasmicInheritance
  INVOLVES: MitochondrialGenome
}

RULE OrganelleInheritanceRule {
  IF genetic_information IS_ORGANELLAR
  THEN inheritance_pattern MAY_DIFFER_FROM nuclear_Mendelian_inheritance
}

# ============================================================
# RECOMBINATION
# ============================================================

PROCESS GeneticRecombination {
  REARRANGES: GeneticMaterial
  MAY_CREATE: NewAllelicCombinations
  DURING: GameteFormation
}

PROCESS CrossingOver {
  SUBPROCESS_OF: GeneticRecombination
  OCCURS_BETWEEN: HomologousChromosomes
}

RULE RecombinationInheritanceRule {
  IF CrossingOver occurs_between_linked_loci
  THEN offspring MAY_RECEIVE recombinant_haplotype
}

# ============================================================
# MUTATION
# ============================================================

PROCESS Mutation {
  CREATES: NewGeneticVariant
  MAY_OCCUR_IN: [Germline, SomaticCell]
}

ENTITY GermlineMutation {
  MAY_BE_TRANSMITTED_TO: Offspring
}

ENTITY SomaticMutation {
  GENERALLY_NOT_TRANSMITTED_THROUGH: Gametes
  EXCEPT_IF germline_involved
}

RULE HeritableMutationRule {
  IF Mutation occurs_in_germline
     AND mutated_gamete contributes_to_offspring
  THEN mutation MAY_BE inherited
}

# ============================================================
# EPIGENETIC INHERITANCE
# ============================================================

ENTITY EpigeneticState {
  MODULATES: GeneExpression
  WITHOUT_REQUIRING: DNASequenceChange
}

PROCESS EpigeneticInheritance {
  MAY_TRANSMIT: EpigeneticState
  ACROSS: CellDivisionOrGeneration
}

RULE EpigeneticInheritanceConstraint {
  IF epigenetic_state persists_across_generations
  THEN transgenerational_inheritance REQUIRES evidence
  beyond direct_exposure_or_developmental_carryover
}

# ============================================================
# GENOMIC IMPRINTING
# ============================================================

PROCESS GenomicImprinting {
  IS_A: ParentOfOriginDependentRegulation
  AFFECTS: AllelicExpression
}

ENTITY ImprintedGene {
  EXPRESSION_DEPENDS_ON: ParentOfOrigin
}

RULE ImprintingRule {
  IF allele_expression differs_by_parent_of_origin
     AND epigenetic_mechanism IS_SUPPORTED
  THEN imprinting MAY_BE_PRESENT
}

# ============================================================
# POLYGENIC HEREDITY
# ============================================================

ENTITY PolygenicInheritance {
  SUBCLASS_OF: HeredityPattern
  INVOLVES: MultipleGeneticLoci
}

ENTITY ComplexTrait {
  INFLUENCED_BY: [
    MultipleGenes,
    Environment,
    GeneGeneInteraction,
    GeneEnvironmentInteraction
  ]
}

RULE ComplexInheritanceConstraint {
  IF Trait IS_COMPLEX
  THEN DO_NOT_ASSUME single_locus_Mendelian_model
}

# ============================================================
# PENETRANCE AND EXPRESSIVITY
# ============================================================

ENTITY Penetrance {
  DESCRIBES: ProbabilityOfPhenotypeGivenGenotype
}

ENTITY Expressivity {
  DESCRIBES: DegreeOfPhenotypicExpression
}

RULE PenetranceRule {
  IF genotype IS_INHERITED
     AND penetrance < 1
  THEN phenotype MAY_NOT_BE observed
}

# ============================================================
# PEDIGREE
# ============================================================

ENTITY Pedigree {
  REPRESENTS: FamilyRelationships
  MAY_TRACK: [Phenotype, Genotype, Inheritance]
}

ENTITY Proband {
  IS_A: Individual
  ROLE: IndexIndividual
}

PROCESS PedigreeAnalysis {
  EVALUATES: HeredityPattern
  USING: Pedigree
}

RULE PedigreeConstraint {
  IF family_pattern IS_COMPATIBLE_WITH inheritance_model
  THEN model MAY_BE_SUPPORTED
  BUT compatibility != proof
}

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

ENTITY Heritability {
  DESCRIBES: PopulationSpecificVarianceRelationship
  FOR: Trait
  DEPENDS_ON: [Population, Environment]
}

RULE HeritabilityDistinction {
  Heritability != Heredity
  Heritability != IndividualGeneticDeterminism
}

# ============================================================
# ENVIRONMENT
# ============================================================

ENTITY Environment {
  MAY_MODIFY: Phenotype
  DOES_NOT_NECESSARILY_CHANGE: Genotype
}

ENTITY GeneEnvironmentInteraction {
  RELATES: Genotype
  AND: Environment
  THROUGH: PhenotypicOutcome
}

RULE EnvironmentRule {
  IF inherited_genotype produces_different_phenotypes_across_environments
  THEN environmental_modulation MAY_BE_SUPPORTED
}

# ============================================================
# POPULATION TRANSMISSION
# ============================================================

ENTITY AlleleFrequency {
  DESCRIBES: FrequencyOfAllele
  WITHIN: Population
}

PROCESS PopulationInheritance {
  TRANSMITS: Alleles
  ACROSS: Generations
  MAY_BE_MODIFIED_BY: [
    NaturalSelection,
    GeneticDrift,
    GeneFlow,
    Mutation
  ]
}

RULE PopulationTransmissionRule {
  AlleleFrequency(t+1) :=
    function(
      inheritance,
      selection,
      drift,
      migration,
      mutation
    )
}

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

ENTITY Evidence {
  TYPES: [
    PedigreeEvidence,
    BreedingEvidence,
    MolecularEvidence,
    GenomicEvidence,
    CytogeneticEvidence,
    PopulationEvidence,
    EpigeneticEvidence,
    ExperimentalEvidence,
    StatisticalEvidence,
    LiteratureEvidence
  ]
}

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

RULE EvidenceConflict {
  IF EvidenceSources CONFLICT
  THEN {
    PRESERVE competing_inheritance_models
    RECORD pedigree_context
    RECORD reproductive_mode
    RECORD locus_and_allele
    RECORD penetrance
    RECORD environmental_context
    RECORD provenance
    REDUCE confidence
    REQUIRE further_validation
  }
}

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

RELATION Parent TRANSMITS GeneticInformation TO Offspring
RELATION Genome CONTAINS Chromosome
RELATION Chromosome CONTAINS Gene
RELATION Gene HAS_ALLELE Allele
RELATION Allele CONTRIBUTES_TO Genotype
RELATION Genotype MAY_CONTRIBUTE_TO Phenotype
RELATION Gamete CARRIES Allele
RELATION Fertilization COMBINES Gametes
RELATION Mutation MAY_CREATE HeritableVariation
RELATION Recombination MAY_CREATE NewAllelicCombination

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

SEMANTIC_EQUIVALENCE {
  "heredity" ~= "genetic inheritance"
  "inheritance" ~= "transmission of genetic information" WHEN biological_context_is_defined
  "heritable" ~= "capable of genetic transmission" WHEN genetic_context_is_defined
  "parental transmission" ~= "inheritance from parent"
  "vertical transmission" ~= "parent-to-offspring genetic transmission" WHEN genetics_context
}

RULE EquivalenceConstraint {
  IF terms ARE semantic_equivalents
  THEN preserve_parent_offspring_relationship()
  AND preserve_locus_and_allele()
  AND preserve_reproductive_mode()
  AND preserve_generation()
  AND prevent_false_identity()
}

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

CONFIDENCE HeredityAssertion {
  INPUTS: [
    pedigree_support,
    breeding_support,
    molecular_support,
    genomic_support,
    cytogenetic_support,
    population_support,
    experimental_support,
    replication,
    source_independence,
    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 ParentOffspringInference {
  IF Parent HAS Allele
     AND Offspring HAS same_Allele
     AND transmission_path IS_COMPATIBLE
  THEN inheritance_from_Parent MAY_BE_SUPPORTED
  WITH confidence := derive(Evidence)
}

RULE GameteTransmissionInference {
  IF Gamete carries Allele
     AND Gamete contributes_to Zygote
  THEN Zygote receives Allele
}

RULE MendelianInference {
  IF trait_pattern matches_simple_segregation
     AND locus_and_allele_model IS_SUPPORTED
  THEN MendelianInheritance MAY_BE_SUPPORTED
}

RULE OrganelleInference {
  IF inherited_variant resides_in organellar_genome
  THEN organellar_inheritance_model SHOULD_BE_EVALUATED
}

RULE CausalityConstraint {
  IF inherited_variant ASSOCIATED_WITH Phenotype
  THEN DO_NOT_INFER variant_causes_phenotype
  WITHOUT causal_evidence
}

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

QUERY HeredityLookup(trait_or_gene) {
  RETURN [
    gene,
    locus,
    alleles,
    inheritance_pattern,
    parental_transmission,
    genotype,
    phenotype,
    penetrance,
    expressivity,
    pedigree_evidence,
    molecular_evidence,
    confidence
  ]
}

QUERY ParentOffspringTransmission(parent, offspring, locus) {
  RETURN [
    parental_alleles,
    offspring_alleles,
    compatible_gametes,
    transmission_path,
    recombination_context,
    mutation_context,
    evidence,
    confidence
  ]
}

QUERY PedigreeHeredityLookup(pedigree_identifier) {
  RETURN [
    individuals,
    relationships,
    phenotypes,
    genotypes,
    candidate_inheritance_models,
    contradictions,
    penetrance_assumptions,
    evidence,
    confidence
  ]
}

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

UPDATE_MODEL {
  ON new_heredity_evidence:
    validate_provenance()
    identify_organism()
    normalize_gene_locus_and_allele_identifiers()
    capture_parent_offspring_relationships()
    capture_reproductive_mode()
    capture_pedigree_structure()
    capture_penetrance_and_expressivity()
    capture_environmental_context()
    evaluate_recombination_and_mutation()
    compare_inheritance_models()
    preserve_conflicting_evidence()
    recalculate_confidence()
    regenerate_heredity_relationships()
    update_flow_hash()
}

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

AI_CONSUMPTION {
  MODE: FormalSemanticReasoning
  PARSE_AS: ExecutableFlowAlgebra

  PRIORITIES: [
    parent_offspring_relationship,
    genetic_information,
    gene_and_locus,
    allele_identity,
    genotype,
    inheritance_pattern,
    reproductive_mode,
    pedigree_context,
    evidence_provenance,
    confidence
  ]

  REQUIREMENTS: [
    distinguish_heredity_from_heritability,
    distinguish_gene_from_allele,
    distinguish_genotype_from_phenotype,
    preserve_parent_offspring_relationship,
    preserve_generation,
    preserve_reproductive_mode,
    account_for_recombination_and_mutation,
    account_for_penetrance_and_environment,
    distinguish_association_from_causation,
    avoid_unsupported_transgenerational_epigenetic_inference
  ]
}

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

VALIDATE {
  REQUIRE Heredity
  REQUIRE GeneticInformation
  REQUIRE Parent
  REQUIRE Offspring
  REQUIRE Gene
  REQUIRE Allele
  REQUIRE Genotype
  REQUIRE Phenotype
  REQUIRE Gamete
  REQUIRE Fertilization
  REQUIRE Evidence
  REQUIRE CONFIDENCE
  REQUIRE SEMANTIC_EQUIVALENCE
  REQUIRE UPDATE_MODEL
  REQUIRE AI_CONSUMPTION

  ASSERT Heredity != Heritability
  ASSERT Gene != Allele
  ASSERT Genotype != Phenotype
  ASSERT inherited_variant != proof_of_phenotypic_causation
  ASSERT pedigree_compatibility != proof
}

# ============================================================
# 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 "HeredityOntology"