Plant Genetics Ontology

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

flow "PlantGeneticsOntology" v1.0

ENTITY PlantGeneticsOntology {
 TYPE: BiologicalOntology
 DOMAIN: Botany
 SUBJECT: PlantGenetics
 PURPOSE: FormalSemanticRepresentation
}

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

ENTITY PlantGenetics {
 STUDIES: HeredityAndGeneticVariation
 IN: Plants
 INCLUDES: [GenomeStructure, GeneFunction, Inheritance, Recombination, Variation, PopulationGenetics, QuantitativeGenetics]
}

ENTITY PlantGenome {
 STORES: HeritableGeneticInformation
 MAY_INCLUDE: [NuclearGenome, PlastidGenome, MitochondrialGenome]
}

ENTITY NuclearGenome { ORGANIZED_IN: NuclearChromosomes }
ENTITY PlastidGenome { LOCATED_IN: Plastid }
ENTITY MitochondrialGenome { LOCATED_IN: Mitochondrion }

RULE GenomeCompartmentConstraint {
 NuclearGenome != PlastidGenome
 NuclearGenome != MitochondrialGenome
}

ENTITY Chromosome {
 CONTAINS: DNA
 CARRIES: GenesAndRegulatoryRegions
}

ENTITY PlantGene {
 IS_A: HeritableGenomicUnit
 MAY_ENCODE: [Protein, FunctionalRNA]
 MAY_HAVE: RegulatoryElements
}

ENTITY Locus {
 IS_A: GenomicPosition
 MAY_CONTAIN: GeneOrGeneticMarker
}

ENTITY Allele {
 IS_A: AlternativeSequenceState
 AT: Locus
}

ENTITY Genotype {
 DESCRIBES: AllelicOrGenomicState
}

ENTITY Phenotype {
 DESCRIBES: ObservableOrMeasurableTraitState
 RESULTS_FROM: [Genotype, Environment, Development, Interaction]
}

RULE GenotypePhenotypeConstraint {
 Genotype != Phenotype
 genotype_alone != complete_phenotype_explanation
}

PROCESS GeneExpression {
 INCLUDES: [Transcription, RNAProcessing, Translation]
}

PROCESS Transcription {
 PRODUCES: RNA
 FROM: DNA_Template
}

PROCESS Translation {
 PRODUCES: Protein
 FROM: MessengerRNA
}

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

ENTITY TranscriptionFactor {
 MAY_MODULATE: PlantGeneExpression
}

ENTITY GeneRegulatoryNetwork {
 CONNECTS: GenesRegulatorsAndSignals
}

RULE ExpressionFunctionConstraint {
 differential_gene_expression != causal_gene_function
 WITHOUT perturbation_or_mechanistic_evidence
}

ENTITY EpigeneticState {
 MAY_INCLUDE: [DNA_Methylation, HistoneModification, ChromatinAccessibility]
 MAY_MODULATE: GeneExpression
}

PROCESS DNA_Methylation {
 MAY_INFLUENCE: GeneRegulation
}

PROCESS HistoneModification {
 MAY_INFLUENCE: GeneAccessibility
}

ENTITY MendelianInheritance {
 DESCRIBES: SegregationOfDiscreteAlleles
 UNDER: ApplicableGeneticModel
}

ENTITY HomozygousGenotype {
 HAS: SameAllelicState
 AT: DefinedLocus
}

ENTITY HeterozygousGenotype {
 HAS: DifferentAllelicStates
 AT: DefinedLocus
}

RULE DominanceConstraint {
 dominance_is_relationship_between_allelic_effects
 AND NOT intrinsic_universal_property_of_allele
}

PROCESS Meiosis {
 PRODUCES: HaploidReproductiveCellsOrSpores
 INVOLVES: ChromosomeSegregationAndRecombination
}

PROCESS Segregation {
 DISTRIBUTES: HomologousChromosomesOrAlleles
 INTO: MeioticProducts
}

PROCESS IndependentAssortment {
 DISTRIBUTES: UnlinkedOrEffectivelyIndependentLoci
 AMONG: MeioticProducts
}

PROCESS Recombination {
 EXCHANGES: GeneticMaterial
 BETWEEN: HomologousChromosomes
 MAY_GENERATE: NewAlleleCombinations
}

ENTITY Crossover {
 IS_A: MeioticRecombinationEvent
}

ENTITY RecombinationFrequency {
 ESTIMATES: GeneticLinkage
 BETWEEN: Loci
}

ENTITY GeneticLinkage {
 OCCURS_WHEN: LociAreInheritedTogetherMoreOftenThanExpectedUnderIndependence
}

ENTITY GeneticMap {
 ORDERS: Loci
 USING: RecombinationOrMolecularInformation
}

RULE LinkageConstraint {
 physical_distance != recombination_distance
}

ENTITY InheritancePattern {
 MAY_BE: [Mendelian, Cytoplasmic, MaternalEffect, Quantitative, Epigenetic]
}

ENTITY CytoplasmicInheritance {
 INVOLVES: PlastidOrMitochondrialGeneticInformation
}

ENTITY MaternalEffect {
 OCCURS_WHEN: MaternalGenotypeInfluencesOffspringPhenotype
 THROUGH: MaternalProductsOrEnvironment
}

RULE MaternalInheritanceConstraint {
 MaternalEffect != CytoplasmicInheritance
}

PROCESS Mutation {
 CHANGES: GeneticSequence
 MAY_GENERATE: NewAllele
}

ENTITY GeneticVariation {
 MAY_INCLUDE: [SingleNucleotideVariant, Indel, StructuralVariant, CopyNumberVariation, TransposableElementVariation, PloidyVariation]
}

ENTITY SingleNucleotideVariant {
 ABBREVIATION: SNV
 CHANGES: SingleNucleotidePosition
}

ENTITY StructuralVariant {
 CHANGES: LargerGenomicStructure
}

ENTITY CopyNumberVariation {
 CHANGES: NumberOfCopies
 OF: GenomicRegion
}

ENTITY TransposableElement {
 IS_A: MobileGeneticElement
 MAY_MOVE_OR_COPY: WithinGenome
}

PROCESS Transposition {
 CHANGES: TransposableElementLocationOrCopyNumber
}

ENTITY Polyploidy {
 DESCRIBES: MoreThanTwoCompleteChromosomeSets
 COMMON_IN: PlantEvolution
}

ENTITY Autopolyploid {
 DERIVES_PRIMARILY_FROM: ChromosomeSetMultiplicationWithinLineage
}

ENTITY Allopolyploid {
 DERIVES_FROM: HybridizationBetweenDistinctLineages
 PLUS: GenomeDuplicationOrEquivalentStabilization
}

PROCESS WholeGenomeDuplication {
 ABBREVIATION: WGD
 DUPLICATES: EntireGenome
}

RULE PolyploidConstraint {
 Polyploidy != SimpleGeneDuplication
}

ENTITY PlantPopulation {
 COMPOSED_OF: PlantIndividuals
}

ENTITY AlleleFrequency {
 DESCRIBES: FrequencyOfAllele
 IN: Population
}

PROCESS NaturalSelection {
 CHANGES: AlleleOrGenotypeFrequencies
 THROUGH: DifferentialReproductiveSuccess
}

PROCESS GeneticDrift {
 CHANGES: AlleleFrequency
 THROUGH: StochasticSampling
}

PROCESS GeneFlow {
 MOVES: Alleles
 BETWEEN: Populations
 THROUGH: PollenSeedOrPropaguleMovement
}

ENTITY PopulationStructure {
 DESCRIBES: NonrandomDistributionOfGeneticVariation
 AMONG: Populations
}

RULE PopulationAssociationConstraint {
 allele_frequency_difference != adaptive_causality
 WITHOUT selection_functional_or_environmental_evidence
}

ENTITY QuantitativeTrait {
 HAS: ContinuousOrPolygenicVariation
}

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

PROCESS QTLMapping {
 IDENTIFIES: GenomicRegionsAssociatedWithTraitVariation
}

PROCESS GenomeWideAssociationStudy {
 ABBREVIATION: GWAS
 TESTS: MarkerTraitAssociations
}

RULE AssociationConstraint {
 marker_trait_association != causal_variant
 WITHOUT fine_mapping_functional_or_mechanistic_evidence
}

ENTITY Heritability {
 DESCRIBES: FractionOfPhenotypicVarianceAssociatedWithGeneticVariance
 IN: DefinedPopulationAndEnvironment
}

RULE HeritabilityConstraint {
 Heritability != TraitImmutability
}

ENTITY GenotypeEnvironmentInteraction {
 ABBREVIATION: GxE
 OCCURS_WHEN: GenotypicEffectsDependOnEnvironment
}

ENTITY PhenotypicPlasticity {
 DESCRIBES: PhenotypicChange
 OF: Genotype
 ACROSS: Environments
}

RULE PlasticityConstraint {
 PhenotypicPlasticity != GeneticChange
}

ENTITY MolecularMarker {
 MAY_BE: [SNPMarker, Microsatellite, IndelMarker, StructuralVariantMarker]
 IDENTIFIES: GenomicVariation
}

PROCESS Genotyping {
 DETERMINES: GeneticState
 AT: OneOrMoreLoci
}

PROCESS DNASequencing {
 DETERMINES: NucleotideSequence
}

PROCESS WholeGenomeSequencing {
 ABBREVIATION: WGS
 DETERMINES: BroadGenomeSequence
}

PROCESS Transcriptomics {
 MEASURES: RNAExpression
}

PROCESS Epigenomics {
 MEASURES: GenomeScaleEpigeneticFeatures
}

ENTITY ReferenceGenome {
 PROVIDES: CoordinateAndSequenceFramework
 FOR: GenomicAnalysis
}

RULE ReferenceConstraint {
 ReferenceGenome != CompleteGeneticDiversityOfSpecies
}

ENTITY Pangenome {
 REPRESENTS: GenomicDiversityAcrossMultipleIndividualsOrAccessions
 MAY_INCLUDE: [CoreGenes, VariableGenes, StructuralVariation]
}

ENTITY PlantBreeding {
 USES: GeneticVariationAndSelection
 TO_CHANGE: PlantTraits
}

PROCESS ArtificialSelection {
 CHANGES: BreedingPopulation
 BY: HumanSelectedReproductiveContribution
}

PROCESS Crossing {
 COMBINES: ParentalGenomes
 THROUGH: SexualReproduction
}

PROCESS Backcrossing {
 CROSSES: HybridOrDescendant
 WITH: RecurrentParentOrRelatedGenotype
}

PROCESS MarkerAssistedSelection {
 USES: GeneticMarkers
 TO_SUPPORT: BreedingSelection
}

PROCESS GenomicSelection {
 USES: GenomeWideMarkerInformation
 TO_PREDICT: BreedingValueOrTraitPerformance
}

ENTITY GeneticTransformation {
 INTRODUCES: GeneticMaterial
 INTO: PlantCellOrGenome
}

ENTITY GenomeEditing {
 MODIFIES: DefinedGenomicTarget
}

RULE EditingConstraint {
 edited_sequence != demonstrated_trait_effect
 WITHOUT phenotypic_and_functional_validation
}

PROCESS PlantGeneticsMeasurement {
 MAY_MEASURE: [Genotype, AlleleFrequency, GeneExpression, RecombinationFrequency, Ploidy, GeneticDiversity, TraitAssociation]
 MAY_USE: [Sequencing, Genotyping, Cytogenetics, Transcriptomics, GeneticCross, Mapping, AssociationAnalysis]
}

ENTITY Evidence {
 TYPES: [GeneticEvidence, GenomicEvidence, MolecularEvidence, ExpressionEvidence, MappingEvidence, AssociationEvidence, FunctionalEvidence, CytogeneticEvidence, PopulationEvidence, BreedingEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_plant_genetic_models
  RECORD plant_taxon
  RECORD population_or_genotype
  RECORD tissue_and_developmental_stage
  RECORD environment
  RECORD reference_genome
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION PlantGenome CONTAINS PlantGene
RELATION PlantGene OCCURS_AT Locus
RELATION Locus MAY_HAVE Allele
RELATION Genotype CONTRIBUTES_TO Phenotype
RELATION Meiosis PRODUCES GeneticSegregation
RELATION Recombination MODIFIES AlleleCombinations
RELATION Mutation GENERATES GeneticVariation
RELATION NaturalSelection MAY_CHANGE AlleleFrequency
RELATION GeneFlow MOVES AllelesBetweenPopulations
RELATION QuantitativeTraitLocus MAY_ASSOCIATE_WITH QuantitativeTrait

SEMANTIC_EQUIVALENCE {
 "plant genetics" ~= "study of heredity and genetic variation in plants"
 "allele" ~= "alternative genetic state at a locus"
 "QTL" ~= "quantitative trait locus"
 "GWAS" ~= "genome-wide association study"
 "GxE" ~= "genotype-by-environment interaction"
 "WGD" ~= "whole-genome duplication"
 "WGS" ~= "whole-genome sequencing"
}

CONFIDENCE PlantGeneticsAssertion {
 INPUTS: [genetic_support, genomic_support, molecular_support, expression_support, mapping_support, association_support, functional_support, cytogenetic_support, population_support, experimental_support, 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"
}

RULE InheritanceInference {
 IF parental_genotypes_and_offspring_genotypes follow_reproducible_segregation_pattern
 THEN InheritancePattern MAY_BE_SUPPORTED
}

RULE LinkageInference {
 IF loci_cosegregate_more_often_than_expected_under_independence
 THEN GeneticLinkage MAY_BE_SUPPORTED
}

RULE QTLInference {
 IF genotype_at_region statistically_associates_with quantitative_trait
 IN validated_mapping_population
 THEN QuantitativeTraitLocus MAY_BE_SUPPORTED
 BUT causal_gene MAY_REMAIN_UNRESOLVED
}

RULE GeneFunctionInference {
 IF gene_perturbation reproducibly_changes phenotype
 AND rescue_or_mechanistic_evidence_supports_relationship
 THEN causal_gene_function MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF marker_or_expression_state correlates_with plant_trait
 THEN DO_NOT_INFER causal_variant_or_gene_function
 WITHOUT functional_or_interventional_evidence
}

QUERY PlantGeneticsLookup(context_identifier) {
 RETURN [plant_taxon, genome, chromosomes, genes, loci, alleles, genotype, phenotype, inheritance, recombination, variation, population_genetics, quantitative_genetics, evidence, confidence]
}

QUERY PlantGeneLookup(gene_identifier) {
 RETURN [genomic_location, alleles, regulatory_elements, expression, molecular_function, phenotype_associations, perturbation_evidence, evolutionary_context, evidence, confidence]
}

QUERY PlantPopulationGeneticsLookup(population_identifier) {
 RETURN [allele_frequencies, genetic_diversity, population_structure, gene_flow, drift, selection, environment, sampling_context, evidence, confidence]
}

UPDATE_MODEL {
 ON new_plant_genetics_evidence:
  validate_provenance()
  identify_plant_taxon_population_genotype_tissue_and_environment()
  normalize_gene_locus_allele_marker_trait_and_reference_identifiers()
  capture_ploidy_and_genome_compartment()
  capture_reference_genome_method_and_timepoint()
  map_genome_chromosome_gene_locus_and_allele_relationships()
  map_expression_epigenetic_and_regulatory_relationships()
  map_meiosis_segregation_linkage_and_recombination()
  map_mutation_structural_variation_transposable_elements_and_polyploidy()
  map_population_genetics_quantitative_traits_QTL_and_GWAS()
  map_breeding_transformation_and_genome_editing_relationships()
  compare_existing_plant_genetic_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_plant_genetics_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [plant_taxon, genome, genome_compartment, chromosome, gene, locus, allele, genotype, phenotype, inheritance, variation, population_context, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_species_taxon_population_genotype_and_environmental_context, preserve_ploidy_and_genome_compartment, preserve_reference_genome_and_method, distinguish_genotype_from_phenotype, distinguish_gene_expression_from_causal_function, distinguish_maternal_effect_from_cytoplasmic_inheritance, distinguish_physical_distance_from_recombination_distance, distinguish_polyploidy_from_gene_duplication, distinguish_marker_association_from_causal_variant, distinguish_heritability_from_trait_immutability, distinguish_phenotypic_plasticity_from_genetic_change, distinguish_correlation_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE PlantGenetics
 REQUIRE PlantGenome
 REQUIRE Chromosome
 REQUIRE PlantGene
 REQUIRE Locus
 REQUIRE Allele
 REQUIRE Genotype
 REQUIRE Phenotype
 REQUIRE GeneExpression
 REQUIRE Meiosis
 REQUIRE Segregation
 REQUIRE Recombination
 REQUIRE Mutation
 REQUIRE GeneticVariation
 REQUIRE PlantPopulation
 REQUIRE AlleleFrequency
 REQUIRE QuantitativeTrait
 REQUIRE QuantitativeTraitLocus
 REQUIRE PlantGeneticsMeasurement
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT NuclearGenome != PlastidGenome
 ASSERT NuclearGenome != MitochondrialGenome
 ASSERT Genotype != Phenotype
 ASSERT differential_gene_expression != causal_gene_function
 ASSERT MaternalEffect != CytoplasmicInheritance
 ASSERT physical_distance != recombination_distance
 ASSERT Polyploidy != SimpleGeneDuplication
 ASSERT marker_trait_association != causal_variant
 ASSERT Heritability != TraitImmutability
 ASSERT PhenotypicPlasticity != GeneticChange
 ASSERT correlation != causation
}

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 "PlantGeneticsOntology"