Growth Ontology

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

flow "GrowthOntology" v1.0

ENTITY GrowthOntology {
 TYPE: BiologicalOntology
 DOMAIN: DevelopmentalBiology
 SUBJECT: BiologicalGrowth
 PURPOSE: FormalSemanticRepresentation
}

PAGE {
 TITLE: "Growth Ontology"
 PARENT_DOMAIN: "Developmental Biology"
 CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/developmental-biology/growth-ontology.html"
 AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY BiologicalGrowth {
 IS_A: DevelopmentalProcess
 INCREASES: [Size, Mass, CellNumber, TissueVolume]
 MAY_OCCUR_AT: [CellularLevel, TissueLevel, OrganLevel, OrganismLevel]
}

ENTITY GrowthState {
 DESCRIBES: CurrentGrowthCondition
 HAS: [Size, Mass, Rate, DevelopmentalStage, Timepoint]
}

ENTITY GrowthRate {
 DESCRIBES: ChangeInGrowthVariablePerTime
}

RULE GrowthRateRule {
 GrowthRate := change(GrowthVariable) / change(Time)
}

ENTITY GrowthVariable {
 MAY_BE: [CellNumber, CellSize, TissueVolume, OrganSize, BodyMass, Length]
}

RULE GrowthDefinitionConstraint {
 growth != development
 growth IS_ONE_COMPONENT_OF development
}

PROCESS CellGrowth {
 INCREASES: CellSizeOrBiomass
}

PROCESS CellProliferation {
 INCREASES: CellNumber
 THROUGH: CellDivision
}

RULE CellGrowthProliferationDistinction {
 CellGrowth != CellProliferation
}

PROCESS BiomassAccumulation {
 INCREASES: BiologicalMaterial
 MAY_INCLUDE: [ProteinSynthesis, LipidSynthesis, NucleicAcidSynthesis, OrganelleBiogenesis]
}

PROCESS CellDivision {
 PRODUCES: DaughterCells
 MAY_CONTRIBUTE_TO: TissueGrowth
}

ENTITY CellCycle {
 COORDINATES: CellGrowthAndDivision
 MAY_INCLUDE: [G1Phase, SPhase, G2Phase, MPhase]
}

RULE CellCycleConstraint {
 cell_cycle_progression != net_tissue_growth
 WITHOUT cell_survival_and_mass_balance_context
}

PROCESS TissueGrowth {
 INCREASES: TissueSizeOrMass
 MAY_RESULT_FROM: [CellProliferation, CellGrowth, ExtracellularMatrixDeposition]
}

ENTITY TissueGrowthRate {
 SUBCLASS_OF: GrowthRate
}

PROCESS OrganGrowth {
 INCREASES: OrganSizeOrMass
 REQUIRES: CoordinatedTissueGrowth
}

PROCESS OrganismalGrowth {
 INCREASES: OrganismSizeOrMass
 INTEGRATES: MultipleOrganAndTissueGrowthProcesses
}

PROCESS DifferentialGrowth {
 OCCURS_WHEN: GrowthRateVariesAcrossSpatialRegions
 MAY_CHANGE: BiologicalShape
}

RULE DifferentialGrowthRule {
 IF RegionA growth_rate != RegionB growth_rate
 THEN tissue_or_organ_geometry MAY_CHANGE
}

ENTITY AllometricGrowth {
 DESCRIBES: DifferentialScalingBetweenBiologicalDimensions
}

ENTITY IsometricGrowth {
 DESCRIBES: ProportionalScalingWithoutShapeChange
 UNDER: DefinedGeometricModel
}

RULE AllometryRelation {
 trait_y MAY_SCALE_AS a * trait_x^b
 WHERE b describes_scaling_exponent
}

ENTITY GrowthFactor {
 IS_A: SignallingMolecule
 MAY_MODULATE: [CellGrowth, Proliferation, Survival, Differentiation]
}

ENTITY GrowthFactorReceptor {
 BINDS_OR_RESPONDS_TO: GrowthFactor
 INITIATES: SignalTransduction
}

PROCESS GrowthSignalling {
 INTEGRATES: [GrowthFactors, Nutrients, EnergyState, HormonalSignals, MechanicalSignals]
 MODULATES: Growth
}

ENTITY NutrientAvailability {
 MAY_LIMIT_OR_SUPPORT: Growth
}

ENTITY EnergyAvailability {
 MAY_LIMIT_OR_SUPPORT: Growth
}

ENTITY OxygenAvailability {
 MAY_LIMIT: Growth
 IN: OxygenDependentBiologicalContext
}

RULE ResourceConstraint {
 growth_rate MAY_BE_LIMITED_BY [
  nutrient_availability,
  energy_availability,
  oxygen_availability,
  biosynthetic_capacity
 ]
}

ENTITY GrowthHormone {
 ABBREVIATION: GH
 IS_A: Hormone
 MAY_MODULATE: OrganismalGrowthAndMetabolism
}

ENTITY InsulinLikeGrowthFactor {
 ABBREVIATION: IGF
 MAY_MEDIATE: GrowthRelatedSignals
}

ENTITY Insulin {
 MAY_MODULATE: NutrientUtilizationAndAnabolicProcesses
}

ENTITY ThyroidHormone {
 MAY_MODULATE: GrowthDevelopmentAndMetabolicRate
}

PROCESS EndocrineGrowthRegulation {
 INTEGRATES: HormonalSignals
 ACROSS: TissuesAndOrgans
}

RULE HormoneGrowthConstraint {
 hormone_concentration != growth_effect
 WITHOUT receptor_tissue_and_developmental_context
}

ENTITY GeneRegulatoryNetwork {
 CONTROLS: GrowthRelatedGeneExpression
}

ENTITY GrowthRegulatoryGene {
 MAY_MODULATE: [CellCycle, Biosynthesis, Metabolism, GrowthSignalling]
}

PROCESS GrowthGeneExpression {
 VARIES_WITH: [CellType, Tissue, DevelopmentalStage, NutritionalState]
}

RULE ExpressionConstraint {
 growth_related_gene_expression != causal_growth_function
 WITHOUT functional_or_perturbation_evidence
}

ENTITY EpigeneticState {
 MAY_MODULATE: GrowthRelatedGeneExpression
}

PROCESS EpigeneticRegulation {
 MAY_CHANGE: GrowthPotentialOrGrowthResponse
}

ENTITY StemCell {
 MAY_CONTRIBUTE_TO: TissueGrowth
 THROUGH: [SelfRenewal, ProgenitorProduction]
}

ENTITY ProgenitorCell {
 MAY_CONTRIBUTE_TO: TissueExpansion
 THROUGH: ProliferationAndDifferentiation
}

PROCESS DevelopmentalGrowth {
 OCCURS_DURING: OrganismalDevelopment
 COORDINATES_WITH: [Patterning, Differentiation, Morphogenesis]
}

RULE GrowthPatterningDistinction {
 growth != pattern_formation
 BUT differential_growth MAY_CONTRIBUTE_TO morphogenesis
}

PROCESS CompensatoryGrowth {
 INCREASES: Growth
 AFTER: TissueLossOrReducedGrowth
 IN: ApplicableBiologicalContext
}

PROCESS CatchUpGrowth {
 DESCRIBES: IncreasedGrowthRateFollowingGrowthRestriction
 IN: ApplicableContext
}

PROCESS RegenerativeGrowth {
 CONTRIBUTES_TO: RestorationOfLostOrDamagedStructure
}

ENTITY GrowthPlate {
 IS_A: SpecializedCartilaginousGrowthRegion
 CONTRIBUTES_TO: LongitudinalBoneGrowth
 IN: ApplicableVertebrateContext
}

PROCESS LongitudinalBoneGrowth {
 INCREASES: BoneLength
 THROUGH: GrowthPlateProcesses
}

PROCESS AppositionalGrowth {
 INCREASES: TissueThicknessOrDiameter
 BY: SurfaceOrPeripheralDeposition
}

PROCESS MuscleGrowth {
 MAY_INCLUDE: [Hypertrophy, HyperplasiaInApplicableContext]
}

PROCESS Hypertrophy {
 INCREASES: CellOrTissueSize
 WITHOUT_NECESSARILY_INCREASING: CellNumber
}

PROCESS Hyperplasia {
 INCREASES: CellNumber
 WITHIN: Tissue
}

RULE HypertrophyHyperplasiaDistinction {
 Hypertrophy != Hyperplasia
}

PROCESS AdiposeTissueGrowth {
 MAY_INCLUDE: [AdipocyteHypertrophy, AdipocyteHyperplasia]
}

ENTITY GrowthLimitation {
 MAY_RESULT_FROM: [ResourceLimitation, SignallingConstraint, MechanicalConstraint, DevelopmentalProgram, CellLoss]
}

ENTITY GrowthArrest {
 DESCRIBES: CessationOrStrongReductionOfGrowth
 MAY_BE: [Temporary, Stable, DevelopmentallyProgrammed]
}

ENTITY GrowthPlateau {
 OCCURS_WHEN: NetGrowthApproachesZero
 UNDER: DefinedConditions
}

PROCESS GrowthHomeostasis {
 BALANCES: [CellProduction, CellGrowth, CellLoss, MatrixTurnover]
}

RULE TissueGrowthBalance {
 NetTissueGrowth :=
  CellProduction
  + BiomassGain
  + MatrixGain
  - CellLoss
  - MaterialLoss
}

ENTITY MechanicalLoad {
 MAY_MODULATE: Growth
 THROUGH: Mechanotransduction
}

PROCESS Mechanotransduction {
 CONVERTS: MechanicalStimulus
 INTO: GrowthRegulatoryResponse
}

ENTITY TissueStiffness {
 MAY_INFLUENCE: GrowthAndCellBehaviour
}

RULE MechanicalCausalityConstraint {
 association_between_load_and_growth != causal_mechanism
 WITHOUT mechanical_or_interventional_evidence
}

ENTITY EnvironmentalFactor {
 MAY_INCLUDE: [Temperature, Nutrition, Light, Oxygen, Stressor]
 MAY_MODULATE: Growth
}

PROCESS EnvironmentalGrowthResponse {
 CHANGES: GrowthRateOrPattern
 IN_RESPONSE_TO: EnvironmentalFactor
}

ENTITY GrowthPlasticity {
 DESCRIBES: CapacityForGrowthTrajectoryToChange
 WITH: EnvironmentOrPhysiologicalState
}

ENTITY GrowthRobustness {
 MAINTAINS: GrowthOutcome
 DESPITE: Perturbation
}

ENTITY GrowthTrajectory {
 REPRESENTS: GrowthVariableAcrossTime
}

ENTITY GrowthCurve {
 REPRESENTS: QuantitativeGrowthTrajectory
}

ENTITY ExponentialGrowthModel {
 MAY_DESCRIBE: UnconstrainedPopulationOrCellGrowth
 UNDER: AppropriateConditions
}

ENTITY LogisticGrowthModel {
 MAY_DESCRIBE: GrowthWithEffectiveUpperConstraint
}

ENTITY GompertzGrowthModel {
 MAY_DESCRIBE: SigmoidalGrowth
 IN: AppropriateContext
}

RULE ModelConstraint {
 fitted_growth_model != demonstrated_biological_mechanism
}

PROCESS GrowthMeasurement {
 MAY_MEASURE: [Length, Area, Volume, Mass, CellNumber, CellSize, GrowthRate, Biomass]
 MAY_USE: [Imaging, Morphometry, Weighing, CellCounting, LineageTracing, MolecularAssay]
}

ENTITY GrowthMeasurementContext {
 HAS: [Organism, DevelopmentalStage, TissueOrOrgan, PhysiologicalState, NutritionalState, Method, Unit, Timepoint]
}

RULE MeasurementContextRule {
 IF growth_measurements ARE_COMPARED
 THEN GrowthMeasurementContext MUST_BE preserved
}

ENTITY Evidence {
 TYPES: [GrowthEvidence, MorphometricEvidence, CellularEvidence, MolecularEvidence, EndocrineEvidence, NutritionalEvidence, MechanicalEvidence, LongitudinalEvidence, PerturbationEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_growth_models
  RECORD organism
  RECORD developmental_stage
  RECORD tissue_or_organ
  RECORD physiological_state
  RECORD nutritional_state
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION BiologicalGrowth CHANGES GrowthVariable
RELATION CellGrowth CONTRIBUTES_TO TissueGrowth
RELATION CellProliferation CONTRIBUTES_TO TissueGrowth
RELATION TissueGrowth CONTRIBUTES_TO OrganGrowth
RELATION OrganGrowth CONTRIBUTES_TO OrganismalGrowth
RELATION GrowthFactor REGULATES GrowthSignalling
RELATION EndocrineGrowthRegulation MODULATES BiologicalGrowth
RELATION DifferentialGrowth MAY_DRIVE Morphogenesis
RELATION Mechanotransduction MODULATES GrowthResponse
RELATION GrowthMeasurement QUANTIFIES GrowthState

SEMANTIC_EQUIVALENCE {
 "biological growth" ~= "increase in biological size mass or cell number"
 "growth rate" ~= "change in growth variable per unit time"
 "hypertrophy" ~= "increase in cell or tissue size"
 "hyperplasia" ~= "increase in cell number"
 "allometric growth" ~= "differential scaling of biological traits"
 "growth trajectory" ~= "growth variable represented across time"
}

CONFIDENCE GrowthAssertion {
 INPUTS: [longitudinal_support, morphometric_support, cellular_support, molecular_support, endocrine_support, nutritional_support, mechanical_support, perturbation_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 GrowthInference {
 IF GrowthVariable increases_over_time
 UNDER consistent_measurement_context
 THEN BiologicalGrowth MAY_BE_SUPPORTED
}

RULE ProliferationContributionInference {
 IF cell_number_increases
 AND cell_loss_is_accounted_for
 THEN CellProliferationContributionToGrowth MAY_BE_SUPPORTED
}

RULE DifferentialGrowthInference {
 IF spatial_regions show_different_growth_rates
 AND geometry_changes_correspondingly
 THEN DifferentialGrowth MAY_BE_SUPPORTED
}

RULE RegulatoryInference {
 IF growth_regulator_perturbation reproducibly_changes_growth_rate_or_trajectory
 THEN growth_regulatory_relationship MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF growth_marker correlates_with growth_outcome
 THEN DO_NOT_INFER causal_growth_role
 WITHOUT mechanistic_or_interventional_evidence
}

QUERY GrowthLookup(context_identifier) {
 RETURN [organism, developmental_stage, growth_variable, growth_rate, cell_growth, proliferation, tissue_growth, organ_growth, endocrine_regulation, resources, mechanics, measurements, evidence, confidence]
}

QUERY GrowthTrajectoryLookup(entity_identifier) {
 RETURN [growth_variable, timepoints, measurements, growth_rate, growth_model, developmental_stage, environmental_context, regulatory_factors, evidence, confidence]
}

QUERY GrowthRegulationLookup(context_identifier) {
 RETURN [growth_factors, hormones, nutrients, energy_state, oxygen_state, gene_regulation, epigenetic_state, mechanical_signals, perturbation_evidence, confidence]
}

UPDATE_MODEL {
 ON new_growth_evidence:
  validate_provenance()
  identify_organism_developmental_stage_and_tissue_or_organ()
  normalize_growth_variable_gene_hormone_and_signal_identifiers()
  normalize_units()
  capture_physiological_nutritional_and_environmental_state()
  capture_measurement_method_and_timepoint()
  map_cell_growth_proliferation_and_cell_loss()
  map_tissue_organ_and_organismal_growth()
  map_endocrine_nutritional_genetic_and_mechanical_regulation()
  fit_growth_models_when_appropriate_without_equating_model_to_mechanism()
  compare_existing_growth_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_growth_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [growth_variable, growth_rate, developmental_stage, cell_growth, proliferation, tissue_and_organ_growth, regulatory_context, resource_state, measurement_context, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_species_context, preserve_developmental_stage, preserve_tissue_or_organ_context, preserve_units_and_timepoint, distinguish_growth_from_development, distinguish_cell_growth_from_cell_proliferation, distinguish_hypertrophy_from_hyperplasia, distinguish_growth_from_pattern_formation, distinguish_fitted_model_from_biological_mechanism, distinguish_correlation_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE BiologicalGrowth
 REQUIRE GrowthState
 REQUIRE GrowthRate
 REQUIRE CellGrowth
 REQUIRE CellProliferation
 REQUIRE TissueGrowth
 REQUIRE OrganGrowth
 REQUIRE OrganismalGrowth
 REQUIRE DifferentialGrowth
 REQUIRE GrowthSignalling
 REQUIRE EndocrineGrowthRegulation
 REQUIRE GrowthTrajectory
 REQUIRE GrowthMeasurement
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT growth != development
 ASSERT CellGrowth != CellProliferation
 ASSERT Hypertrophy != Hyperplasia
 ASSERT growth != pattern_formation
 ASSERT fitted_growth_model != demonstrated_biological_mechanism
 ASSERT correlation != causal_growth_role
}

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 "GrowthOntology"