Genetics Ontology

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

flow "GeneticsOntologyCore" v1.0

# ============================================================
# IDENTITY
# ============================================================

ENTITY GeneticsOntology {
    TYPE: BiologicalOntology
    DOMAIN: Genetics
    SUBJECT: GeneticInheritanceAndVariation
    PURPOSE: FormalSemanticRepresentation
}

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

# ============================================================
# FOUNDATIONAL ENTITIES
# ============================================================

ENTITY GeneticInformation {
    STORED_IN: GeneticMaterial
    TRANSMITTED_BY: Inheritance
    EXPRESSED_THROUGH: GeneExpression
}

ENTITY GeneticMaterial {
    MAY_BE: [DNA, RNA]
    CONTAINS: GeneticInformation
}

ENTITY Genome {
    IS_A: CompleteGeneticInformationSet
    CONTAINS: [Chromosome, Gene, RegulatoryRegion]
}

ENTITY Chromosome {
    PART_OF: Genome
    CONTAINS: Gene
    CARRIES: GeneticInformation
}

ENTITY Gene {
    IS_A: HereditaryInformationUnit
    PART_OF: Genome
    LOCATED_AT: GeneticLocus
    MAY_HAVE: Allele
    MAY_ENCODE: FunctionalGeneProduct
}

ENTITY GeneticLocus {
    IDENTIFIES: PositionOrRegion
    WITHIN: Genome
}

ENTITY Allele {
    IS_A: AlternativeStateAtGeneticLocus
    ASSOCIATED_WITH: GeneOrLocus
}

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

ENTITY Genotype {
    REPRESENTS: GeneticState
    MAY_REFERENCE: [SingleLocus, MultipleLoci, WholeGenome]
    CONTRIBUTES_TO: Phenotype
}

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

ENTITY Trait {
    HAS: PhenotypicState
    MAY_BE: [QualitativeTrait, QuantitativeTrait, ComplexTrait]
}

ENTITY Penetrance {
    DESCRIBES: ProbabilityOfPhenotypeGivenGenotype
}

ENTITY Expressivity {
    DESCRIBES: DegreeOfPhenotypicExpression
}

RULE GenotypePhenotypeMapping {
    Phenotype := function(
        Genotype,
        Environment,
        DevelopmentalContext,
        EpigeneticState
    )
}

# ============================================================
# HEREDITY AND INHERITANCE
# ============================================================

PROCESS Heredity {
    TRANSMITS: GeneticInformation
    FROM: Parent
    TO: Offspring
}

ENTITY InheritancePattern {
    MAY_BE: [
        AutosomalDominant,
        AutosomalRecessive,
        XLinked,
        YLinked,
        Mitochondrial,
        Codominant,
        IncompleteDominance,
        Polygenic
    ]
}

PROCESS Segregation {
    OCCURS_DURING: GameteFormation
    SEPARATES: Alleles
}

PROCESS IndependentAssortment {
    DESCRIBES: TransmissionOfDifferentLoci
    SUBJECT_TO: GeneticLinkage
}

RULE SegregationRule {
    IF organism IS_DIPLOID
       AND locus HAS two_homologous_allelic_copies
    THEN gamete typically_receives one_copy
}

RULE IndependentAssortmentConstraint {
    IF loci ARE_LINKED
    THEN complete_independent_assortment MUST_NOT_BE_ASSUMED
}

# ============================================================
# DOMINANCE RELATIONSHIPS
# ============================================================

ENTITY DominanceRelationship {
    RELATES: Alleles
    WITHIN: DefinedPhenotypicContext
}

CLASS CompleteDominance {
    SUBCLASS_OF: DominanceRelationship
}

CLASS IncompleteDominance {
    SUBCLASS_OF: DominanceRelationship
}

CLASS Codominance {
    SUBCLASS_OF: DominanceRelationship
}

RULE DominanceContextRule {
    IF AlleleA IS_DOMINANT_TO AlleleB
    THEN relationship MUST_ATTACH [
        locus,
        trait,
        biological_context
    ]
}

# ============================================================
# GENETIC VARIATION
# ============================================================

ENTITY GeneticVariant {
    IS_A: DifferenceFromReferenceGeneticState
    MAY_BE: [
        SingleNucleotideVariant,
        Insertion,
        Deletion,
        Duplication,
        Inversion,
        Translocation,
        CopyNumberVariant
    ]
}

ENTITY Mutation {
    IS_A: GeneticChangeEvent
    MAY_PRODUCE: GeneticVariant
}

CLASS GermlineVariant {
    SUBCLASS_OF: GeneticVariant
    MAY_BE: Heritable
}

CLASS SomaticVariant {
    SUBCLASS_OF: GeneticVariant
    OCCURS_IN: SomaticLineage
}

RULE MutationVariantDistinction {
    Mutation := change_event
    GeneticVariant := observed_or_resulting_state
}

# ============================================================
# RECOMBINATION AND LINKAGE
# ============================================================

PROCESS GeneticRecombination {
    EXCHANGES: GeneticMaterial
    MAY_CREATE: NewAllelicCombinations
}

PROCESS CrossingOver {
    SUBPROCESS_OF: GeneticRecombination
    OCCURS_BETWEEN: HomologousChromosomes
}

ENTITY GeneticLinkage {
    RELATES: GeneticLoci
    DESCRIBES: NonIndependentTransmission
}

ENTITY RecombinationFrequency {
    MEASURES: RecombinantFraction
    MAY_ESTIMATE: GeneticDistance
}

ENTITY GeneticMap {
    ORDERS: GeneticLoci
    MAY_USE: RecombinationFrequency
}

RULE LinkageRule {
    IF loci_are_cotransmitted_more_frequently_than_independent_expectation
    THEN linkage_support := increase(linkage_support)
}

# ============================================================
# MEIOSIS
# ============================================================

PROCESS Meiosis {
    INPUT: DiploidGermlineCell
    OUTPUT: HaploidCells
    INCLUDES: [MeiosisI, MeiosisII]
}

PROCESS MeiosisI {
    SEGREGATES: HomologousChromosomes
    MAY_INCLUDE: CrossingOver
}

PROCESS MeiosisII {
    SEGREGATES: SisterChromatids
}

RULE MeioticInheritanceRule {
    IF Alleles reside_on_homologous_chromosomes
    THEN Meiosis contributes_to allelic_segregation
}

# ============================================================
# MOLECULAR GENETICS
# ============================================================

PROCESS DNAReplication {
    COPIES: DNA
    SUPPORTS: GeneticContinuity
}

PROCESS Transcription {
    INPUT: DNA
    OUTPUT: RNA
}

PROCESS Translation {
    INPUT: mRNA
    OUTPUT: Polypeptide
}

PROCESS GeneExpression {
    INPUT: Gene
    OUTPUT: FunctionalGeneProduct
    MAY_INCLUDE: [Transcription, RNAProcessing, Translation]
}

RELATION Gene EXPRESSED_AS FunctionalGeneProduct
RELATION FunctionalGeneProduct MAY_INFLUENCE Phenotype

# ============================================================
# GENE REGULATION
# ============================================================

ENTITY RegulatoryElement {
    MAY_BE: [Promoter, Enhancer, Silencer]
    MODULATES: GeneExpression
}

ENTITY TranscriptionFactor {
    BINDS: RegulatoryElement
    MAY_MODULATE: Transcription
}

PROCESS GeneRegulation {
    TARGET: GeneExpression
    MAY_INCLUDE: [
        TranscriptionalRegulation,
        PostTranscriptionalRegulation,
        TranslationalRegulation,
        EpigeneticRegulation
    ]
}

# ============================================================
# EPIGENETICS
# ============================================================

ENTITY EpigeneticState {
    MAY_AFFECT: GeneExpression
    WITHOUT_REQUIRING: DNASequenceChange
    MAY_INCLUDE: [
        DNA_Methylation,
        HistoneModification,
        ChromatinState
    ]
}

RULE EpigeneticSequenceConstraint {
    IF EpigeneticState changes
    THEN DO_NOT_INFER GeneticVariant
    UNLESS sequence_change IS_OBSERVED
}

# ============================================================
# COMPLEX AND QUANTITATIVE TRAITS
# ============================================================

ENTITY ComplexTrait {
    SUBCLASS_OF: Trait
    INFLUENCED_BY: [
        MultipleGeneticLoci,
        Environment,
        GeneGeneInteraction,
        GeneEnvironmentInteraction
    ]
}

ENTITY QuantitativeTrait {
    SUBCLASS_OF: Trait
    HAS: ContinuousOrMultifactorialVariation
}

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

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

RULE HeritabilityConstraint {
    IF Heritability IS_ESTIMATED
    THEN DO_NOT_INFER individual_genetic_determination
}

# ============================================================
# GENETIC INTERACTIONS
# ============================================================

ENTITY GeneticInteraction {
    RELATES: GeneticPerturbations
    THROUGH: CombinedPhenotypicEffect
}

CLASS Epistasis {
    SUBCLASS_OF: GeneticInteraction
    OCCURS_WHEN: EffectOfOneLocusDependsOnAnother
}

RULE GeneticInteractionRule {
    IF combined_effect != expected_combination_of_individual_effects
    THEN GeneticInteraction MAY_BE_SUPPORTED
}

# ============================================================
# POPULATION GENETICS
# ============================================================

ENTITY Population {
    COMPOSED_OF: Individuals
    HAS: AlleleFrequencyDistribution
}

ENTITY AlleleFrequency {
    DESCRIBES: FrequencyOfAllele
    WITHIN: Population
}

PROCESS NaturalSelection {
    MAY_CHANGE: AlleleFrequency
    THROUGH: DifferentialReproductiveSuccess
}

PROCESS GeneticDrift {
    MAY_CHANGE: AlleleFrequency
    THROUGH: SamplingVariation
}

PROCESS GeneFlow {
    TRANSFERS: GeneticVariation
    BETWEEN: Populations
}

RULE AlleleFrequencyDynamics {
    AlleleFrequencyChange MAY_DEPEND_ON [
        NaturalSelection,
        GeneticDrift,
        GeneFlow,
        Mutation,
        MatingStructure
    ]
}

# ============================================================
# PEDIGREE GENETICS
# ============================================================

ENTITY Pedigree {
    REPRESENTS: FamilialRelationships
    MAY_INCLUDE: [Genotype, Phenotype]
}

ENTITY Proband {
    IS_A: Individual
    ROLE: IndexIndividual
}

PROCESS SegregationAnalysis {
    USES: Pedigree
    EVALUATES: InheritanceModel
}

RULE PedigreeInferenceConstraint {
    IF pedigree_pattern IS_COMPATIBLE_WITH inheritance_model
    THEN inheritance_model MAY_BE_SUPPORTED
    BUT compatibility != proof
}

# ============================================================
# GENETIC ASSOCIATION
# ============================================================

ENTITY GeneticAssociation {
    RELATES: GeneticVariant
    TO: PhenotypeOrTrait
    BASED_ON: StatisticalEvidence
}

PROCESS AssociationStudy {
    TESTS: GeneticAssociation
    WITHIN: Population
}

RULE AssociationCausalityConstraint {
    IF GeneticVariant IS_ASSOCIATED_WITH Trait
    THEN DO_NOT_INFER causation
    UNLESS causal_evidence IS_SUFFICIENT
}

# ============================================================
# GENETIC EVIDENCE
# ============================================================

ENTITY Evidence {
    TYPES: [
        SequencingEvidence,
        PedigreeEvidence,
        FunctionalEvidence,
        PopulationEvidence,
        CytogeneticEvidence,
        MolecularEvidence,
        ExperimentalEvidence,
        ComputationalEvidence,
        LiteratureEvidence
    ]
}

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

RULE EvidenceConflict {
    IF EvidenceSources CONFLICT
    THEN {
        PRESERVE competing_assertions
        RECORD genome_assembly
        RECORD population_context
        RECORD pedigree_context
        RECORD experimental_context
        RECORD provenance
        REDUCE confidence
        REQUIRE further_validation
    }
}

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

RELATION Genome CONTAINS Chromosome
RELATION Chromosome CONTAINS Gene
RELATION Gene LOCATED_AT GeneticLocus
RELATION Gene HAS_ALLELE Allele
RELATION Allele CONTRIBUTES_TO Genotype
RELATION Genotype MAY_INFLUENCE Phenotype
RELATION Mutation MAY_PRODUCE GeneticVariant
RELATION GeneticVariant MAY_AFFECT Gene
RELATION GeneExpression PRODUCES FunctionalGeneProduct
RELATION Heredity TRANSMITS GeneticInformation

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

SEMANTIC_EQUIVALENCE {
    "genetic locus" ~= "locus" WHEN genetics_context_is_defined
    "genetic variant" ~= "sequence variant" WHEN sequence_context_is_defined
    "heredity" ~= "genetic inheritance"
    "recombination" ~= "genetic recombination" WHEN genetics_context_is_defined
    "QTL" ~= "quantitative trait locus"
}

RULE EquivalenceConstraint {
    IF terms ARE semantic_equivalents
    THEN preserve_gene_or_locus_identity()
    AND preserve_genome_assembly()
    AND preserve_population_context()
    AND preserve_inheritance_context()
    AND prevent_false_identity()
}

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

CONFIDENCE GeneticsAssertion {
    INPUTS: [
        sequence_support,
        pedigree_support,
        functional_support,
        population_support,
        experimental_support,
        statistical_support,
        source_independence,
        reproducibility,
        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 AlleleInheritanceInference {
    IF Parent HAS Allele
       AND Offspring HAS same_Allele
       AND inheritance_path IS_COMPATIBLE
    THEN inherited_origin MAY_BE_SUPPORTED
    WITH confidence := derive(Evidence)
}

RULE VariantGeneInference {
    IF GeneticVariant OVERLAPS Gene
    THEN GeneticVariant ASSOCIATED_WITH Gene
    WITH functional_consequence := unresolved_until_evaluated
}

RULE GeneTraitInference {
    IF Gene has_supported_biological_role_in Trait
       AND GeneticVariant functionally_affects Gene
    THEN GeneticVariant MAY_CONTRIBUTE_TO Trait
    WITH causality := evidence_dependent
}

RULE PopulationDifferenceInference {
    IF AlleleFrequency(PopulationA) != AlleleFrequency(PopulationB)
    THEN frequency_difference := observed
    BUT evolutionary_cause := unresolved_without_evidence
}

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

QUERY GeneticsEntityLookup(identifier) {
    RETURN [
        entity_type,
        identity,
        genomic_location,
        alleles,
        variants,
        genotype,
        phenotype,
        inheritance,
        population_context,
        evidence,
        confidence
    ]
}

QUERY GeneInheritanceLookup(gene_identifier) {
    RETURN [
        gene,
        locus,
        alleles,
        inheritance_patterns,
        associated_traits,
        penetrance,
        expressivity,
        pedigree_evidence,
        population_evidence,
        confidence
    ]
}

QUERY TraitGeneticsLookup(trait_identifier) {
    RETURN [
        associated_genes,
        associated_variants,
        QTLs,
        inheritance_models,
        genetic_interactions,
        environmental_context,
        population_context,
        evidence,
        confidence
    ]
}

QUERY VariantGeneticsLookup(variant_identifier) {
    RETURN [
        genomic_location,
        reference_state,
        alternate_state,
        affected_gene,
        inheritance_context,
        molecular_consequence,
        trait_associations,
        population_frequency,
        evidence,
        confidence
    ]
}

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

UPDATE_MODEL {
    ON new_genetics_evidence:
        validate_provenance()
        identify_organism()
        identify_genome_assembly()
        normalize_gene_locus_and_variant_identifiers()
        normalize_genomic_coordinates()
        capture_genotype_and_phenotype_context()
        capture_pedigree_context()
        capture_population_context()
        capture_environmental_context()
        compare_existing_assertions()
        preserve_conflicting_evidence()
        recalculate_confidence()
        regenerate_genetic_relationships()
        update_flow_hash()
}

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

AI_CONSUMPTION {
    MODE: FormalSemanticReasoning
    PARSE_AS: ExecutableFlowAlgebra

    PRIORITIES: [
        genetic_entity_identity,
        gene_and_locus_context,
        allele_identity,
        genotype,
        phenotype,
        inheritance,
        population_context,
        evidence_provenance,
        confidence,
        semantic_equivalence
    ]

    REQUIREMENTS: [
        distinguish_gene_from_locus,
        distinguish_gene_from_allele,
        distinguish_genotype_from_phenotype,
        distinguish_mutation_event_from_variant_state,
        preserve_species_context,
        preserve_genome_assembly,
        preserve_pedigree_context,
        preserve_population_context,
        distinguish_association_from_causation,
        distinguish_heritability_from_individual_determinism
    ]
}

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

VALIDATE {
    REQUIRE GeneticInformation
    REQUIRE Genome
    REQUIRE Chromosome
    REQUIRE Gene
    REQUIRE GeneticLocus
    REQUIRE Allele
    REQUIRE Genotype
    REQUIRE Phenotype
    REQUIRE Heredity
    REQUIRE GeneticVariant
    REQUIRE Evidence
    REQUIRE CONFIDENCE
    REQUIRE SEMANTIC_EQUIVALENCE
    REQUIRE UPDATE_MODEL
    REQUIRE AI_CONSUMPTION

    ASSERT Gene != Allele
    ASSERT Gene != GeneticLocus
    ASSERT Genotype != Phenotype
    ASSERT Mutation != GeneticVariant
    ASSERT GeneticAssociation != CausalProof
    ASSERT Heritability != IndividualDeterminism
}

# ============================================================
# 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 "GeneticsOntologyCore"