Recombination Ontology

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

flow "RecombinationOntology" v1.0

ENTITY RecombinationOntology {
  TYPE: BiologicalOntology
  DOMAIN: Genetics
  SUBJECT: GeneticRecombination
  PURPOSE: FormalSemanticRepresentation
}

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

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

PROCESS GeneticRecombination {
  IS_A: GeneticProcess
  REARRANGES: GeneticMaterial
  MAY_CREATE: NewAllelicCombinations
  MAY_OCCUR_DURING: [Meiosis, DNARepair, HorizontalGeneticExchange]
}

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

ENTITY RecombinantSequence {
  RESULTS_FROM: GeneticRecombination
  CONTAINS: NewCombinationOfGeneticSegments
}

ENTITY RecombinantChromosome {
  IS_A: Chromosome
  RESULTS_FROM: Recombination
}

RULE RecombinationDistinction {
  GeneticRecombination REARRANGES genetic_information
  Mutation CHANGES sequence_state
  RECOMBINATION DOES_NOT_NECESSARILY_CREATE new_mutation
}

# ============================================================
# HOMOLOGOUS RECOMBINATION
# ============================================================

PROCESS HomologousRecombination {
  SUBCLASS_OF: GeneticRecombination
  REQUIRES: HomologousOrHighlySimilarSequence
  MAY_OCCUR_IN: [Meiosis, DNARepair]
}

ENTITY HomologousSequence {
  SHARES: SequenceSimilarity
  WITH: AnotherSequence
}

ENTITY HomologousChromosome {
  CARRIES: CorrespondingGeneticLoci
  MAY_PARTICIPATE_IN: MeioticRecombination
}

RULE HomologyRequirement {
  IF process == HomologousRecombination
  THEN homologous_sequence_alignment IS_REQUIRED
}

# ============================================================
# MEIOTIC RECOMBINATION
# ============================================================

PROCESS MeioticRecombination {
  SUBCLASS_OF: HomologousRecombination
  OCCURS_DURING: Meiosis
  INVOLVES: HomologousChromosomes
  MAY_PRODUCE: RecombinantGametes
}

PROCESS Synapsis {
  ALIGNS: HomologousChromosomes
  DURING: MeioticProphase
}

ENTITY SynaptonemalComplex {
  ASSOCIATED_WITH: SynapsedHomologousChromosomes
  SUPPORTS: MeioticChromosomeOrganization
}

PROCESS CrossingOver {
  SUBPROCESS_OF: MeioticRecombination
  EXCHANGES: ChromosomalSegments
  BETWEEN: HomologousChromatids
}

ENTITY Chiasma {
  REPRESENTS: CytologicalAssociation
  RELATED_TO: CrossingOver
}

RULE CrossingOverRule {
  IF homologous_chromatids exchange_corresponding_segments
  THEN recombinant_chromatids MAY_FORM
}

# ============================================================
# DOUBLE-STRAND BREAKS
# ============================================================

ENTITY DoubleStrandBreak {
  ABBREVIATION: DSB
  IS_A: DNA_Lesion
  MAY_INITIATE: HomologousRecombination
}

PROCESS EndResection {
  PROCESSES: DoubleStrandBreak
  PRODUCES: SingleStrandedDNARegion
}

PROCESS StrandInvasion {
  USES: SingleStrandedDNA
  SEARCHES_FOR: HomologousTemplate
  FORMS: HeteroduplexIntermediate
}

ENTITY HeteroduplexDNA {
  CONTAINS: StrandsFromDifferentDNA_Molecules
  MAY_FORM_DURING: HomologousRecombination
}

RULE DSBRepairPathway {
  DoubleStrandBreak
    -> EndResection
    -> HomologySearch
    -> StrandInvasion
    -> DNA_Synthesis
    -> IntermediateResolution
}

# ============================================================
# HOLLIDAY JUNCTIONS
# ============================================================

ENTITY HollidayJunction {
  IS_A: BranchedDNAIntermediate
  MAY_FORM_DURING: HomologousRecombination
}

PROCESS BranchMigration {
  MOVES: HollidayJunction
  ALONG: HomologousDNA
}

PROCESS JunctionResolution {
  RESOLVES: HollidayJunction
  MAY_PRODUCE: [CrossoverProduct, NonCrossoverProduct]
}

RULE ResolutionOutcome {
  IF recombination_intermediate IS_RESOLVED
  THEN outcome MAY_BE crossover OR noncrossover
  DEPENDING_ON resolution_pathway
}

# ============================================================
# CROSSOVER AND NON-CROSSOVER
# ============================================================

ENTITY Crossover {
  RESULTS_IN: ReciprocalExchangeOfFlankingMarkers
}

ENTITY NonCrossover {
  RESULTS_FROM: HomologousRecombination
  WITHOUT: ReciprocalExchangeOfFlankingMarkers
}

RULE CrossoverDistinction {
  Crossover != all_homologous_recombination_events
  NonCrossover IS_POSSIBLE
}

# ============================================================
# GENE CONVERSION
# ============================================================

PROCESS GeneConversion {
  IS_A: NonReciprocalSequenceTransfer
  MAY_RESULT_FROM: HeteroduplexRepair
}

ENTITY ConversionTract {
  DEFINES: RegionAffectedByGeneConversion
}

RULE GeneConversionRule {
  IF heteroduplex_mismatch IS_REPAIRED_USING one_sequence_as_template
  THEN nonreciprocal_allelic_conversion MAY_OCCUR
}

# ============================================================
# RECOMBINATION FREQUENCY
# ============================================================

ENTITY RecombinationFrequency {
  DESCRIBES: FractionOfRecombinantProducts
  BETWEEN: GeneticMarkers
}

ENTITY GeneticDistance {
  ESTIMATED_FROM: RecombinationFrequency
  UNIT_MAY_BE: Centimorgan
}

ENTITY Centimorgan {
  SYMBOL: cM
  IS_A: GeneticMapUnit
}

RULE RecombinationFrequencyRule {
  recombination_frequency :=
    recombinant_offspring_or_gametes / total_offspring_or_gametes
}

RULE MappingConstraint {
  IF loci_are_far_apart
  THEN observed_recombination_frequency MAY_UNDERESTIMATE multiple_crossovers
}

# ============================================================
# GENETIC LINKAGE
# ============================================================

ENTITY GeneticLinkage {
  RELATES: Loci
  ON: SameChromosome
  MAY_REDUCE: IndependentAssortment
}

RULE LinkageRecombinationRule {
  IF loci_are_close_together
  THEN recombination_frequency TENDS_TO_BE lower
  THAN more_distant_loci
  subject_to_recombination_landscape
}

# ============================================================
# RECOMBINATION HOTSPOTS
# ============================================================

ENTITY RecombinationHotspot {
  IS_A: GenomicRegion
  HAS: ElevatedRecombinationRate
  RELATIVE_TO: LocalBackground
}

ENTITY RecombinationColdspot {
  IS_A: GenomicRegion
  HAS: ReducedRecombinationRate
}

RULE HotspotInference {
  IF local_recombination_rate > genomic_background
     AND evidence_is_sufficient
  THEN region MAY_BE RecombinationHotspot
}

# ============================================================
# RECOMBINATION RATE
# ============================================================

ENTITY RecombinationRate {
  DESCRIBES: RecombinationFrequencyPerPhysicalOrGeneticDistance
  MAY_VARY_BY: [
    Species,
    Sex,
    Chromosome,
    GenomicRegion,
    DevelopmentalContext
  ]
}

RULE RateContextRule {
  IF RecombinationRate IS_REPORTED
  THEN preserve [
    organism,
    sex_if_relevant,
    chromosome,
    genomic_interval,
    measurement_method
  ]
}

# ============================================================
# RECOMBINATION INTERFERENCE
# ============================================================

ENTITY CrossoverInterference {
  DESCRIBES: InfluenceOfOneCrossoverOnNearbyCrossoverProbability
}

ENTITY CoefficientOfCoincidence {
  COMPARES: ObservedDoubleCrossovers
  TO: ExpectedDoubleCrossovers
}

RULE InterferenceRule {
  IF nearby_crossovers occur_less_often_than_independent_expectation
  THEN positive_crossover_interference MAY_BE_SUPPORTED
}

# ============================================================
# MITOTIC RECOMBINATION
# ============================================================

PROCESS MitoticRecombination {
  SUBCLASS_OF: HomologousRecombination
  OCCURS_IN: SomaticOrMitoticallyDividingCells
  MAY_RESULT_IN: LossOfHeterozygosity
}

ENTITY LossOfHeterozygosity {
  ABBREVIATION: LOH
  DESCRIBES: LossOfOneAllelicStateInRegion
}

RULE MitoticRecombinationRule {
  IF homologous_exchange occurs_during_mitotic_cell_cycle
  THEN descendant_cells MAY_HAVE altered_allelic_configuration
}

# ============================================================
# SITE-SPECIFIC RECOMBINATION
# ============================================================

PROCESS SiteSpecificRecombination {
  SUBCLASS_OF: GeneticRecombination
  OCCURS_AT: DefinedRecognitionSites
  CATALYSED_BY: Recombinase
}

ENTITY Recombinase {
  IS_A: Enzyme
  CATALYSES: Recombination
}

RULE SiteSpecificRule {
  IF Recombinase recognizes_compatible_sites
  THEN DNA_segments MAY_BE rearranged
  ACCORDING_TO site_orientation_and_mechanism
}

# ============================================================
# NON-HOMOLOGOUS RECOMBINATION
# ============================================================

PROCESS NonHomologousRecombination {
  SUBCLASS_OF: GeneticRecombination
  DOES_NOT_REQUIRE: ExtensiveSequenceHomology
  MAY_CREATE: StructuralRearrangement
}

RULE NonHomologousConstraint {
  IF recombination_occurs_without_extensive_homology
  THEN DO_NOT_CLASSIFY_AS HomologousRecombination
}

# ============================================================
# RECOMBINATION AND DNA REPAIR
# ============================================================

PROCESS DNARepair {
  MAY_USE: HomologousRecombination
  TO_REPAIR: DoubleStrandBreak
}

ENTITY SisterChromatid {
  MAY_SERVE_AS: HomologousRepairTemplate
}

RULE RepairTemplateRule {
  IF SisterChromatid IS_AVAILABLE
  THEN homologous_repair MAY_USE SisterChromatid
  WITH generally_high_sequence_similarity
}

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

ENTITY LinkageDisequilibrium {
  ABBREVIATION: LD
  DESCRIBES: NonRandomAssociationOfAllelesAtDifferentLoci
}

RULE RecombinationLDRule {
  IF recombination_occurs_between_loci
  THEN LinkageDisequilibrium MAY_DECREASE
  OVER_GENERATIONS
  subject_to_selection_drift_and_demography
}

ENTITY Haplotype {
  IS_A: CombinationOfAlleles
  LOCATED_ON: SameChromosomalSegment
}

RELATION Recombination MAY_BREAK Haplotype
RELATION Recombination MAY_CREATE NewHaplotype

# ============================================================
# EVOLUTIONARY ROLE
# ============================================================

PROCESS Evolution {
  USES: HeritableVariation
}

RULE EvolutionaryRecombinationRule {
  IF Recombination creates_new_allelic_combinations
  THEN population_genetic_variation MAY_BE_RESHUFFLED
  AND evolutionary_response MAY_CHANGE
}

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

ENTITY Evidence {
  TYPES: [
    GeneticCrossEvidence,
    CytologicalEvidence,
    MolecularEvidence,
    SequencingEvidence,
    PopulationGenomicEvidence,
    DNARepairEvidence,
    ExperimentalEvidence,
    ComputationalEvidence,
    LiteratureEvidence
  ]
}

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

RULE EvidenceConflict {
  IF EvidenceSources CONFLICT
  THEN {
    PRESERVE competing_recombination_models
    RECORD organism
    RECORD chromosome
    RECORD genomic_interval
    RECORD meiotic_or_mitotic_context
    RECORD detection_method
    RECORD provenance
    REDUCE confidence
    REQUIRE further_validation
  }
}

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

RELATION GeneticRecombination REARRANGES GeneticMaterial
RELATION MeioticRecombination OCCURS_DURING Meiosis
RELATION CrossingOver EXCHANGES ChromosomalSegments
RELATION HomologousRecombination MAY_REPAIR DoubleStrandBreak
RELATION RecombinationFrequency ESTIMATES GeneticDistance
RELATION GeneticLinkage MODIFIES RecombinationObservation
RELATION Recombination MAY_CHANGE Haplotype
RELATION Recombination MAY_REDUCE LinkageDisequilibrium

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

SEMANTIC_EQUIVALENCE {
  "genetic recombination" ~= "recombination" WHEN genetics_context_is_defined
  "crossing over" ~= "meiotic crossover" WHEN meiotic_context_is_defined
  "recombination frequency" ~= "recombinant fraction" WHEN measurement_context_is_defined
  "genetic map distance" ~= "recombination-based genetic distance"
  "cM" ~= "centimorgan"
}

RULE EquivalenceConstraint {
  IF terms ARE semantic_equivalents
  THEN preserve_organism()
  AND preserve_chromosome()
  AND preserve_genomic_interval()
  AND preserve_meiotic_or_mitotic_context()
  AND prevent_false_identity()
}

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

CONFIDENCE RecombinationAssertion {
  INPUTS: [
    genetic_cross_support,
    molecular_support,
    cytological_support,
    sequencing_support,
    population_support,
    experimental_reproducibility,
    source_independence,
    interval_definition_quality,
    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 RecombinantInference {
  IF offspring_or_gamete has_allelic_combination
     not_matching_parental_haplotypes
  THEN recombinant_status MAY_BE_SUPPORTED
}

RULE CrossoverInference {
  IF reciprocal_exchange_of_flanking_markers IS_DETECTED
  THEN Crossover MAY_BE_INFERRED
}

RULE GeneticDistanceInference {
  IF valid_recombination_frequency IS_AVAILABLE
  THEN GeneticDistance MAY_BE_ESTIMATED
  WITH mapping_function_and_limitations
}

RULE HotspotInferenceRule {
  IF local_recombination_rate significantly_exceeds_background
  THEN RecombinationHotspot MAY_BE_SUPPORTED
}

RULE RepairInference {
  IF DoubleStrandBreak repair uses_homologous_template
     AND recombination_intermediates_are_supported
  THEN HomologousRecombinationRepair MAY_BE_INFERRED
}

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

QUERY RecombinationLookup(genomic_region) {
  RETURN [
    organism,
    chromosome,
    genomic_interval,
    recombination_rate,
    crossover_frequency,
    hotspots,
    coldspots,
    linkage,
    haplotypes,
    evidence,
    confidence
  ]
}

QUERY LocusPairRecombinationLookup(locus_a, locus_b) {
  RETURN [
    physical_distance,
    recombination_frequency,
    genetic_distance,
    linkage_status,
    crossover_evidence,
    interference,
    mapping_model,
    confidence
  ]
}

QUERY RecombinationEventLookup(event_identifier) {
  RETURN [
    event_type,
    meiotic_or_mitotic_context,
    participating_sequences,
    breakpoints,
    crossover_or_noncrossover,
    gene_conversion,
    resulting_sequences,
    evidence,
    confidence
  ]
}

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

UPDATE_MODEL {
  ON new_recombination_evidence:
    validate_provenance()
    identify_organism()
    identify_genome_assembly()
    normalize_chromosome_and_coordinates()
    normalize_locus_and_marker_identifiers()
    classify_recombination_type()
    capture_meiotic_or_mitotic_context()
    calculate_recombination_frequency()
    estimate_genetic_distance()
    compare_existing_models()
    preserve_conflicting_evidence()
    recalculate_confidence()
    regenerate_linkage_and_haplotype_relationships()
    update_flow_hash()
}

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

AI_CONSUMPTION {
  MODE: FormalSemanticReasoning
  PARSE_AS: ExecutableFlowAlgebra

  PRIORITIES: [
    recombination_type,
    participating_sequences,
    chromosome_context,
    genomic_interval,
    meiotic_or_mitotic_context,
    recombination_frequency,
    linkage,
    crossover_status,
    evidence_provenance,
    confidence
  ]

  REQUIREMENTS: [
    distinguish_recombination_from_mutation,
    distinguish_homologous_from_nonhomologous_recombination,
    distinguish_crossover_from_noncrossover,
    preserve_species_context,
    preserve_genome_assembly,
    preserve_chromosome_and_interval,
    preserve_meiotic_or_mitotic_context,
    distinguish_recombination_frequency_from_physical_distance,
    account_for_multiple_crossovers,
    distinguish_observed_from_inferred_recombination
  ]
}

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

VALIDATE {
  REQUIRE GeneticRecombination
  REQUIRE HomologousRecombination
  REQUIRE MeioticRecombination
  REQUIRE CrossingOver
  REQUIRE RecombinationFrequency
  REQUIRE GeneticDistance
  REQUIRE GeneticLinkage
  REQUIRE RecombinationHotspot
  REQUIRE Evidence
  REQUIRE CONFIDENCE
  REQUIRE SEMANTIC_EQUIVALENCE
  REQUIRE UPDATE_MODEL
  REQUIRE AI_CONSUMPTION

  ASSERT GeneticRecombination != Mutation
  ASSERT Crossover != all_recombination
  ASSERT RecombinationFrequency != PhysicalDistance
  ASSERT linked_loci != zero_recombination
  ASSERT recombinant_pattern != proof_of_specific_mechanism
}

# ============================================================
# 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 "RecombinationOntology"