Genetics

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

flow "GeneticsOntology" v1.0

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

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

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

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

ENTITY Genetics {
    STUDIES: [
        Heredity,
        GeneticVariation,
        GeneFunction,
        GenomeOrganization,
        Inheritance,
        GenotypePhenotypeRelationships
    ]
}

ENTITY Gene {
    IS_A: HereditaryInformationUnit
    PART_OF: Genome
    LOCATED_ON: Chromosome
    MAY_HAVE: Allele
    MAY_INFLUENCE: Phenotype
}

ENTITY Genome {
    CONTAINS: GeneticInformation
    ORGANIZED_INTO: Chromosome
}

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

ENTITY Allele {
    IS_A: AlternativeFormOfGeneticLocus
    ASSOCIATED_WITH: Gene
    CONTRIBUTES_TO: Genotype
}

ENTITY Genotype {
    COMPOSED_OF: AllelicState
    MAY_CONTRIBUTE_TO: Phenotype
}

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

# ============================================================
# HEREDITY
# ============================================================

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

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

RULE InheritanceRule {
    IF Allele IS_PRESENT_IN transmissible_germline
       AND gamete contributes_to_offspring
    THEN Allele MAY_BE inherited
}

# ============================================================
# MENDELIAN GENETICS
# ============================================================

ENTITY MendelianGenetics {
    STUDIES: InheritanceOfDiscreteTraits
    USES: [Allele, Genotype, Phenotype]
}

PROPERTY Dominance {
    RELATES: AllelesAtLocus
}

PROPERTY Recessiveness {
    RELATES: AllelesAtLocus
}

PROCESS Segregation {
    SEPARATES: Alleles
    DURING: GameteFormation
}

PROCESS IndependentAssortment {
    APPLIES_TO: SuitableLoci
    DESCRIBES: IndependentTransmission
    SUBJECT_TO: GeneticLinkage
}

RULE SegregationRule {
    IF organism IS_DIPLOID
       AND locus HAS two_alleles
    THEN gamete typically_receives one_allele_at_locus
}

RULE LinkageConstraint {
    IF loci ARE_GENETICALLY_LINKED
    THEN DO_NOT_ASSUME complete_independent_assortment
}

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

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

ENTITY Penetrance {
    DESCRIBES: ProbabilityOfPhenotypeGivenGenotype
}

ENTITY Expressivity {
    DESCRIBES: DegreeOfPhenotypicExpression
}

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

RULE NonDeterminismRule {
    IF Genotype IS_KNOWN
    THEN DO_NOT_ASSUME Phenotype IS_FULLY_DETERMINED
    UNLESS model_and_evidence_support_determinism
}

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

ENTITY GeneticVariation {
    DESCRIBES: SequenceOrStructuralDifference
    MAY_INCLUDE: [
        SingleNucleotideVariant,
        Insertion,
        Deletion,
        Duplication,
        Inversion,
        Translocation,
        CopyNumberVariation
    ]
}

ENTITY Mutation {
    MAY_CREATE: GeneticVariation
    MAY_OCCUR_IN: [Germline, SomaticCell]
}

RELATION Gene HAS_VARIANT GeneticVariation
RELATION GeneticVariation MAY_AFFECT GeneFunction
RELATION GeneticVariation MAY_AFFECT GeneExpression

RULE VariantEffectRule {
    IF GeneticVariation overlaps_functional_region
    THEN consequence := evaluate(
        genomic_context,
        transcript_context,
        regulatory_context,
        functional_evidence
    )
}

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

PROCESS GeneticRecombination {
    EXCHANGES: GeneticMaterial
    MAY_CREATE: NewAllelicCombinations
}

ENTITY GeneticLinkage {
    RELATES: Loci
    BASED_ON: CoTransmissionFrequency
}

ENTITY RecombinationFrequency {
    ESTIMATES: GeneticDistance
    WITHIN: ApplicableRange
}

ENTITY GeneticMap {
    ORDERS: GeneticLoci
    MAY_USE: RecombinationFrequency
}

RULE LinkageInference {
    IF loci_are_cotransmitted_more_often_than_expected_under_independence
    THEN GeneticLinkage MAY_BE_SUPPORTED
}

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

PROCESS Meiosis {
    PRODUCES: HaploidCells
    INCLUDES: [MeiosisI, MeiosisII]
    ENABLES: GeneticSegregation
}

PROCESS MeiosisI {
    SEGREGATES: HomologousChromosomes
    MAY_INCLUDE: CrossingOver
}

PROCESS MeiosisII {
    SEGREGATES: SisterChromatids
}

PROCESS CrossingOver {
    OCCURS_BETWEEN: HomologousChromosomes
    CONTRIBUTES_TO: GeneticRecombination
}

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

ENTITY PopulationGenetics {
    STUDIES: AlleleFrequencyChange
    WITHIN: Population
}

ENTITY AlleleFrequency {
    DESCRIBES: RelativeFrequencyOfAllele
    WITHIN: Population
}

PROCESS NaturalSelection {
    MAY_CHANGE: AlleleFrequency
    THROUGH: DifferentialReproductiveSuccess
}

PROCESS GeneticDrift {
    MAY_CHANGE: AlleleFrequency
    THROUGH: SamplingVariation
}

PROCESS GeneFlow {
    TRANSFERS: Alleles
    BETWEEN: Populations
}

PROCESS MutationPressure {
    INTRODUCES: NewAlleles
}

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

# ============================================================
# QUANTITATIVE GENETICS
# ============================================================

ENTITY QuantitativeGenetics {
    STUDIES: QuantitativeTraits
    MAY_MODEL: [GeneticEffects, EnvironmentalEffects]
}

ENTITY QuantitativeTrait {
    HAS: ContinuousOrMultifactorialVariation
    MAY_BE_INFLUENCED_BY: MultipleLoci
}

ENTITY Heritability {
    DESCRIBES: PopulationSpecificVarianceRelationship
    DEPENDS_ON: PopulationAndEnvironment
}

RULE HeritabilityConstraint {
    IF Heritability IS_ESTIMATED
    THEN DO_NOT_INTERPRET_AS individual_determinism
    AND preserve_population_context()
}

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

ENTITY MolecularGenetics {
    STUDIES: GeneticProcessesAtMolecularLevel
    INCLUDES: [
        DNAReplication,
        Transcription,
        Translation,
        GeneExpression,
        Mutation,
        DNARepair
    ]
}

PROCESS DNAReplication {
    COPIES: GeneticMaterial
}

PROCESS Transcription {
    TRANSFERS_INFORMATION_FROM: DNA
    TO: RNA
}

PROCESS Translation {
    DECODES: mRNA
    PRODUCES: Polypeptide
}

PROCESS GeneExpression {
    USES: GeneticInformation
    PRODUCES: FunctionalGeneProduct
}

# ============================================================
# REGULATORY GENETICS
# ============================================================

ENTITY GeneRegulation {
    MODULATES: GeneExpression
    MAY_INCLUDE: [
        TranscriptionalRegulation,
        PostTranscriptionalRegulation,
        TranslationalRegulation,
        EpigeneticRegulation
    ]
}

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

ENTITY TranscriptionFactor {
    BINDS: RegulatoryElement
    MAY_ACTIVATE_OR_REPRESS: Transcription
}

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

ENTITY Epigenetics {
    STUDIES: StableOrHeritableRegulatoryStates
    WITHOUT_REQUIRING: DNASequenceChange
}

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

RULE EpigeneticDistinction {
    IF EpigeneticState changes
    THEN DO_NOT_INFER DNASequenceChange
}

# ============================================================
# COMPLEX TRAITS
# ============================================================

ENTITY ComplexTrait {
    INFLUENCED_BY: [
        MultipleGenes,
        Environment,
        GeneGeneInteractions,
        GeneEnvironmentInteractions
    ]
}

ENTITY PolygenicTrait {
    SUBCLASS_OF: ComplexTrait
    INFLUENCED_BY: MultipleGeneticLoci
}

RULE ComplexTraitRule {
    IF Trait IS ComplexTrait
    THEN single_gene_explanation SHOULD_NOT_BE_ASSUMED
}

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

ENTITY GeneticInteraction {
    RELATES: GeneticPerturbations
    THROUGH: CombinedPhenotypicEffect
}

CLASS Epistasis {
    SUBCLASS_OF: GeneticInteraction
    OCCURS_WHEN: EffectOfOneLocusDependsOnAnotherLocus
}

RULE EpistasisRule {
    IF combined_genotype_effect != expectation_from_individual_effects
    THEN GeneticInteraction MAY_BE_PRESENT
}

# ============================================================
# PEDIGREE AND FAMILY INHERITANCE
# ============================================================

ENTITY Pedigree {
    REPRESENTS: FamilialRelationshipsAndTraits
    MAY_SUPPORT: InheritanceAnalysis
}

ENTITY Proband {
    IS_A: Individual
    ROLE: IndexIndividualInPedigree
}

PROCESS SegregationAnalysis {
    USES: Pedigree
    EVALUATES: InheritanceModel
}

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

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

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

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

RULE EvidenceConflict {
    IF EvidenceSources CONFLICT
    THEN {
        PRESERVE competing_assertions
        RECORD organism_context
        RECORD population_context
        RECORD genomic_context
        RECORD methodology
        RECORD provenance
        REDUCE confidence
        REQUIRE further_validation
    }
}

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

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 Mutation MAY_CREATE GeneticVariation
RELATION GeneticVariation MAY_AFFECT Trait
RELATION GeneExpression PRODUCES FunctionalGeneProduct
RELATION Heredity TRANSMITS GeneticInformation

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

SEMANTIC_EQUIVALENCE {
    "genetics" ~= "science of heredity and genetic variation"
    "genetic variant" ~= "sequence variant" WHEN context == genomic_difference
    "allelic variant" ~= "allele" WHEN context == locus_specific_state
    "genetic inheritance" ~= "heredity"
    "genetic recombination" ~= "recombination" WHEN genetic_context_is_defined
}

RULE EquivalenceConstraint {
    IF terms ARE semantic_equivalents
    THEN preserve_locus_identity()
    AND preserve_organism_context()
    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_reproducibility,
        source_independence,
        statistical_support,
        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 InheritanceInference {
    IF Allele IS_PRESENT_IN Parent
       AND Allele IS_DETECTED_IN Offspring
       AND inheritance_path IS_COMPATIBLE
    THEN inherited_origin MAY_BE_SUPPORTED
    WITH confidence := derive(Evidence)
}

RULE GeneTraitInference {
    IF GeneticVariation affects Gene
       AND Gene has_supported_role_in Trait
    THEN GeneticVariation MAY_BE_ASSOCIATED_WITH Trait
}

RULE PopulationInference {
    IF AlleleFrequency differs_between_populations
    THEN difference := observed
    BUT cause MUST_NOT_BE_ASSUMED_WITHOUT_EVIDENCE
}

RULE CausalityConstraint {
    IF GeneticVariant ASSOCIATED_WITH Phenotype
    THEN DO_NOT_INFER causal_effect
    UNLESS causal_evidence IS_SUFFICIENT
}

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

QUERY GeneLookup(gene_identifier) {
    RETURN [
        identity,
        genomic_location,
        alleles,
        variants,
        gene_products,
        expression,
        functions,
        trait_associations,
        inheritance_information,
        evidence,
        confidence
    ]
}

QUERY TraitGeneticsLookup(trait_identifier) {
    RETURN [
        associated_genes,
        associated_variants,
        inheritance_patterns,
        penetrance,
        expressivity,
        environmental_factors,
        population_context,
        evidence,
        confidence
    ]
}

QUERY VariantLookup(variant_identifier) {
    RETURN [
        genomic_location,
        reference_allele,
        alternate_allele,
        affected_gene,
        molecular_consequence,
        inheritance_context,
        population_frequency,
        phenotype_associations,
        evidence,
        confidence
    ]
}

QUERY PedigreeLookup(pedigree_identifier) {
    RETURN [
        individuals,
        relationships,
        phenotypes,
        genotypes,
        segregation_pattern,
        candidate_inheritance_models,
        evidence,
        confidence
    ]
}

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

UPDATE_MODEL {
    ON new_genetic_evidence:
        validate_provenance()
        identify_organism()
        identify_population()
        identify_genome_assembly()
        normalize_gene_and_variant_identifiers()
        normalize_genomic_coordinates()
        capture_pedigree_or_inheritance_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: [
        gene_identity,
        allele_identity,
        genotype,
        phenotype,
        inheritance_context,
        genomic_context,
        population_context,
        evidence_provenance,
        confidence,
        semantic_equivalence
    ]

    REQUIREMENTS: [
        distinguish_gene_from_allele,
        distinguish_genotype_from_phenotype,
        distinguish_mutation_from_variant_state,
        preserve_species_context,
        preserve_genome_assembly,
        preserve_population_context,
        preserve_family_relationship_context,
        distinguish_association_from_causation,
        distinguish_heritability_from_individual_determinism,
        avoid_unsupported_inheritance_inference
    ]
}

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

VALIDATE {
    REQUIRE Genetics
    REQUIRE Gene
    REQUIRE Genome
    REQUIRE Chromosome
    REQUIRE Allele
    REQUIRE Genotype
    REQUIRE Phenotype
    REQUIRE Heredity
    REQUIRE GeneticVariation
    REQUIRE Evidence
    REQUIRE CONFIDENCE
    REQUIRE SEMANTIC_EQUIVALENCE
    REQUIRE UPDATE_MODEL
    REQUIRE AI_CONSUMPTION

    ASSERT Gene != Allele
    ASSERT Genotype != Phenotype
    ASSERT Mutation != GeneticVariation
    ASSERT association != causation
    ASSERT Heritability != individual_determinism
}

# ============================================================
# 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 "GeneticsOntology"