Digestive System Ontology

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

flow "DigestiveSystemOntology" v1.0

ENTITY DigestiveSystemOntology {
 TYPE: BiologicalOntology
 DOMAIN: Physiology
 SUBJECT: DigestiveSystem
 PURPOSE: FormalSemanticRepresentation
}

PAGE {
 TITLE: "Digestive System Ontology"
 PARENT_DOMAIN: "Physiology"
 CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/physiology/digestive-system-ontology.html"
 AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY DigestiveSystem {
 IS_A: PhysiologicalSystem
 FUNCTIONS_IN: [Ingestion, Digestion, Absorption, Motility, Secretion, Elimination]
 COMPOSED_OF: [GastrointestinalTract, AccessoryDigestiveOrgans]
}

ENTITY GastrointestinalTract {
 COMPOSED_OF: [OralCavity, Pharynx, Esophagus, Stomach, SmallIntestine, LargeIntestine, Rectum, AnalCanal]
 TRANSPORTS_AND_PROCESSES: LuminalContents
}

ENTITY AccessoryDigestiveOrgan {
 MAY_INCLUDE: [SalivaryGland, Liver, Gallbladder, Pancreas]
 CONTRIBUTES_TO: Digestion
}

PROCESS Ingestion {
 INTRODUCES: Food
 INTO: DigestiveSystem
}

PROCESS Mastication {
 MECHANICALLY_BREAKS_DOWN: Food
 IN: OralCavity
}

PROCESS Swallowing {
 MOVES: Bolus
 FROM: OralCavity
 TOWARD: Stomach
}

ENTITY Saliva {
 PRODUCED_BY: SalivaryGland
 MAY_CONTAIN: [Water, Electrolytes, Mucins, DigestiveEnzymes]
}

ENTITY Esophagus {
 TRANSPORTS: Bolus
 TO: Stomach
}

PROCESS Peristalsis {
 PROPAGATES: ContractileWave
 MOVES: LuminalContents
}

ENTITY Stomach {
 STORES_AND_MIXES: Food
 SECRETES: GastricContents
 INITIATES_OR_CONTINUES: Digestion
}

ENTITY GastricAcid {
 CONTRIBUTES_TO: LowGastricPH
 MAY_SUPPORT: ProteinDigestionAndDefense
}

ENTITY Pepsin {
 IS_A: Protease
 PARTICIPATES_IN: GastricProteinDigestion
}

PROCESS GastricEmptying {
 MOVES: Chyme
 FROM: Stomach
 TO: SmallIntestine
}

ENTITY SmallIntestine {
 MAY_INCLUDE: [Duodenum, Jejunum, Ileum]
 PRIMARY_SITE_FOR: NutrientDigestionAndAbsorption
}

ENTITY Duodenum {
 RECEIVES: [Chyme, Bile, PancreaticSecretions]
}

ENTITY Jejunum {
 PARTICIPATES_IN: NutrientAbsorption
}

ENTITY Ileum {
 PARTICIPATES_IN: SelectiveNutrientAndBileAcidAbsorption
}

ENTITY IntestinalVillus {
 INCREASES: AbsorptiveSurfaceArea
}

ENTITY Microvillus {
 PART_OF: IntestinalBrushBorder
 INCREASES: AbsorptiveSurfaceArea
}

ENTITY LargeIntestine {
 ABSORBS: [Water, Electrolytes]
 SUPPORTS: MicrobialFermentation
 FORMS: FecalMaterial
}

ENTITY Colon {
 MAJOR_PART_OF: LargeIntestine
}

PROCESS Defecation {
 ELIMINATES: FecalMaterial
}

PROCESS MechanicalDigestion {
 PHYSICALLY_BREAKS_DOWN: Food
 WITHOUT_NECESSARILY_CHANGING: ChemicalIdentity
}

PROCESS ChemicalDigestion {
 BREAKS_DOWN: NutrientMacromolecules
 USING: HydrolysisAndEnzymes
}

ENTITY DigestiveEnzyme {
 IS_A: Enzyme
 CATALYSES: DigestiveReaction
 MAY_BE: [Protease, Lipase, Carbohydrase, Nuclease]
}

PROCESS CarbohydrateDigestion {
 CONVERTS: ComplexCarbohydrates
 TO: AbsorbableSugars
}

PROCESS ProteinDigestion {
 CONVERTS: Proteins
 TO: PeptidesAndAminoAcids
}

PROCESS LipidDigestion {
 CONVERTS: DietaryLipids
 TO: AbsorbableLipidComponents
}

PROCESS NucleicAcidDigestion {
 CONVERTS: NucleicAcids
 TO: SmallerComponents
}

ENTITY Pancreas {
 IS_A: AccessoryDigestiveOrgan
 PRODUCES: PancreaticSecretions
 ALSO_HAS: EndocrineFunction
}

ENTITY PancreaticSecretion {
 MAY_CONTAIN: [DigestiveEnzymes, Bicarbonate]
 ENTERS: SmallIntestine
}

ENTITY Bicarbonate {
 MAY_NEUTRALIZE: GastricAcid
 IN: Duodenum
}

ENTITY Liver {
 IS_A: AccessoryDigestiveOrgan
 PRODUCES: Bile
 PROCESSES: AbsorbedNutrients
}

ENTITY Gallbladder {
 STORES_AND_CONCENTRATES: Bile
}

ENTITY Bile {
 CONTAINS: BileAcids
 SUPPORTS: LipidDigestionAndAbsorption
}

PROCESS Emulsification {
 DISPERSES: Lipid
 INTO: SmallerDroplets
 MAY_INCREASE: SurfaceAreaForLipase
}

PROCESS NutrientAbsorption {
 MOVES: DigestedNutrient
 ACROSS: IntestinalEpithelium
 INTO: BloodOrLymph
}

ENTITY IntestinalEpithelium {
 FORMS: SelectiveBarrier
 MEDIATES: NutrientAbsorption
}

PROCESS MonosaccharideAbsorption {
 MOVES: Monosaccharide
 INTO: Circulation
 MAY_USE: TransportProtein
}

PROCESS AminoAcidAbsorption {
 MOVES: AminoAcid
 INTO: Circulation
 MAY_USE: TransportProtein
}

PROCESS LipidAbsorption {
 MOVES: LipidDerivedProducts
 THROUGH: Enterocyte
 MAY_FORM: Chylomicron
}

ENTITY Chylomicron {
 IS_A: LipoproteinParticle
 TRANSPORTS: DietaryLipids
 THROUGH: LymphAndBlood
}

PROCESS WaterAbsorption {
 MOVES: Water
 ACROSS: IntestinalEpithelium
}

PROCESS ElectrolyteAbsorption {
 MOVES: Electrolyte
 ACROSS: IntestinalEpithelium
}

PROCESS GastrointestinalMotility {
 MOVES_AND_MIXES: LuminalContents
 MAY_INCLUDE: [Peristalsis, Segmentation]
}

PROCESS Segmentation {
 MIXES: IntestinalContents
 MAY_ENHANCE: ContactWithAbsorptiveSurface
}

ENTITY EntericNervousSystem {
 IS_A: NeuralNetwork
 REGULATES: GastrointestinalFunction
}

PROCESS EntericControl {
 MAY_MODULATE: [Motility, Secretion, BloodFlow]
}

ENTITY ParasympatheticInput {
 MAY_MODULATE: DigestiveActivity
}

ENTITY SympatheticInput {
 MAY_MODULATE: DigestiveActivity
}

PROCESS GastrointestinalSecretion {
 RELEASES: [Water, Electrolytes, Mucus, Acid, Bicarbonate, Enzymes]
 INTO: GastrointestinalLumen
}

ENTITY Mucus {
 PROTECTS_AND_LUBRICATES: GastrointestinalSurface
}

ENTITY GastrointestinalHormone {
 IS_A: Hormone
 MAY_REGULATE: [Secretion, Motility, Appetite, PancreaticFunction, BiliaryFunction]
}

ENTITY Gastrin {
 IS_A: GastrointestinalHormone
 MAY_STIMULATE: GastricSecretoryAndMotorFunctions
}

ENTITY Secretin {
 IS_A: GastrointestinalHormone
 MAY_STIMULATE: BicarbonateRichSecretions
}

ENTITY Cholecystokinin {
 ABBREVIATION: CCK
 IS_A: GastrointestinalHormone
 MAY_MODULATE: [PancreaticEnzymeSecretion, GallbladderContraction, GastricEmptying]
}

PROCESS DigestiveEndocrineRegulation {
 COORDINATES: GastrointestinalFunction
 USING: GastrointestinalHormones
}

ENTITY GutMicrobiota {
 OCCUPIES: GastrointestinalTract
 MAY_METABOLIZE: DietaryAndHostDerivedSubstrates
}

PROCESS MicrobialFermentation {
 CONVERTS: FermentableSubstrate
 TO: MicrobialMetabolites
}

ENTITY ShortChainFattyAcid {
 MAY_BE_PRODUCED_BY: MicrobialFermentation
 MAY_BE_ABSORBED_BY: Host
}

RULE MicrobiotaConstraint {
 microbial_association_with_host_state != causal_effect
 WITHOUT functional_or_interventional_evidence
}

ENTITY GastrointestinalBarrier {
 INCLUDES: [EpithelialBarrier, MucusLayer, ImmuneComponents]
 REGULATES: ExchangeBetweenLumenAndInternalEnvironment
}

PROCESS BarrierTransport {
 MAY_BE: [TranscellularTransport, ParacellularTransport]
}

ENTITY SplanchnicCirculation {
 SUPPLIES: DigestiveOrgans
 TRANSPORTS: AbsorbedNutrients
}

ENTITY HepaticPortalCirculation {
 TRANSPORTS: AbsorbedWaterSolubleNutrients
 FROM: GastrointestinalTract
 TO: Liver
}

RELATION NutrientAbsorption FEEDS HepaticPortalCirculation

PROCESS PostprandialResponse {
 OCCURS_AFTER: NutrientIngestion
 MAY_CHANGE: [Motility, Secretion, Hormones, BloodFlow, Metabolism]
}

PROCESS FastingDigestiveState {
 OCCURS_DURING: AbsenceOfRecentNutrientIntake
 MAY_CHANGE: GastrointestinalMotilityAndSecretion
}

RULE DigestiveStateConstraint {
 digestive_measurement MUST_PRESERVE feeding_or_fasting_state
 WHEN relevant
}

PROCESS DigestiveHomeostasis {
 MAINTAINS: [NutrientHandling, FluidBalance, BarrierFunction, LuminalEnvironment]
}

PROCESS DigestiveMeasurement {
 MAY_MEASURE: [Motility, Secretion, Absorption, LuminalPH, EnzymeActivity, TransitTime, NutrientConcentration]
 MAY_USE: [Imaging, Manometry, BreathTesting, Endoscopy, BiochemicalAssay, IsotopeTracing]
}

ENTITY DigestiveMeasurementContext {
 HAS: [Organism, GastrointestinalRegion, FeedingState, Diet, PhysiologicalState, Method, Unit, Timepoint]
}

RULE MeasurementContextRule {
 IF digestive_measurements ARE_COMPARED
 THEN DigestiveMeasurementContext MUST_BE preserved
}

ENTITY Evidence {
 TYPES: [
  PhysiologicalEvidence,
  BiochemicalEvidence,
  NutritionalEvidence,
  MotilityEvidence,
  ImagingEvidence,
  EndoscopicEvidence,
  MicrobiomeEvidence,
  IsotopeTracingEvidence,
  ExperimentalEvidence,
  ComputationalEvidence,
  LiteratureEvidence
 ]
}

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_digestive_models
  RECORD organism
  RECORD gastrointestinal_region
  RECORD feeding_state
  RECORD diet
  RECORD physiological_state
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION DigestiveSystem CONTAINS GastrointestinalTract
RELATION DigestiveSystem USES AccessoryDigestiveOrgans
RELATION Stomach PRODUCES Chyme
RELATION SmallIntestine PERFORMS NutrientAbsorption
RELATION Pancreas PROVIDES PancreaticSecretion
RELATION Liver PRODUCES Bile
RELATION Gallbladder STORES Bile
RELATION EntericNervousSystem REGULATES GastrointestinalFunction
RELATION GastrointestinalHormone REGULATES DigestiveProcess
RELATION GutMicrobiota PARTICIPATES_IN LuminalMetabolism

SEMANTIC_EQUIVALENCE {
 "digestive system" ~= "gastrointestinal digestive system" WHEN physiological_context
 "GI tract" ~= "gastrointestinal tract"
 "digestion" ~= "breakdown of food into absorbable components" WHEN nutritional_context
 "CCK" ~= "cholecystokinin"
 "gut microbiota" ~= "gastrointestinal microbial community" WHEN microbiological_context
}

CONFIDENCE DigestiveSystemAssertion {
 INPUTS: [
  physiological_support,
  biochemical_support,
  absorption_support,
  motility_support,
  secretion_support,
  nutritional_support,
  measurement_quality,
  replication,
  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 DigestionInference {
 IF nutrient_macromolecule decreases
 AND expected_digestive_products increase
 AND appropriate_enzyme_activity IS_PRESENT
 THEN digestive_transformation MAY_BE_SUPPORTED
}

RULE AbsorptionInference {
 IF luminal_nutrient decreases
 AND corresponding_internal_or_portal_nutrient increases
 THEN NutrientAbsorption MAY_BE_SUPPORTED
 WITH transport_and_metabolic_context
}

RULE MotilityInference {
 IF coordinated_contractile_activity moves_luminal_contents
 THEN GastrointestinalMotility MAY_BE_SUPPORTED
}

RULE EndocrineRegulationInference {
 IF gastrointestinal_hormone perturbation reproducibly_changes secretion_or_motility
 THEN endocrine_digestive_regulation MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF digestive_variable correlates_with physiological_outcome
 THEN DO_NOT_INFER causal_relationship
 WITHOUT mechanistic_or_interventional_evidence
}

QUERY DigestiveSystemLookup(context_identifier) {
 RETURN [
  gastrointestinal_regions,
  accessory_organs,
  ingestion,
  digestion,
  secretion,
  motility,
  absorption,
  endocrine_regulation,
  enteric_control,
  microbiota,
  measurements,
  evidence,
  confidence
 ]
}

QUERY DigestiveRegionLookup(region_identifier) {
 RETURN [
  anatomy_context,
  luminal_environment,
  secretions,
  enzymes,
  motility,
  absorbed_nutrients,
  neural_control,
  endocrine_control,
  microbiota,
  evidence,
  confidence
 ]
}

QUERY NutrientDigestionLookup(nutrient_identifier) {
 RETURN [
  substrate,
  digestive_enzymes,
  breakdown_products,
  gastrointestinal_regions,
  absorption_mechanisms,
  transport_route,
  regulation,
  evidence,
  confidence
 ]
}

UPDATE_MODEL {
 ON new_digestive_evidence:
  validate_provenance()
  identify_organism_and_physiological_state()
  normalize_gastrointestinal_region_and_nutrient_identifiers()
  normalize_enzyme_hormone_and_transporter_identifiers()
  capture_feeding_state_and_diet()
  capture_measurement_method_units_and_timepoint()
  map_digestive_reactions_and_secretions()
  map_motility_and_transit()
  map_absorption_and_transport_routes()
  map_enteric_and_endocrine_regulation()
  map_microbiota_relationships()
  compare_existing_digestive_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_digestive_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [
  gastrointestinal_region,
  nutrient_identity,
  digestion,
  secretion,
  motility,
  absorption,
  neural_and_endocrine_control,
  feeding_state,
  measurement_context,
  evidence_provenance,
  confidence
 ]
 REQUIREMENTS: [
  preserve_species_context,
  preserve_gastrointestinal_region,
  preserve_feeding_and_dietary_context,
  preserve_physiological_state,
  distinguish_mechanical_from_chemical_digestion,
  distinguish_digestion_from_absorption,
  distinguish_luminal_concentration_from_absorbed_flux,
  distinguish_microbiota_association_from_causal_effect,
  distinguish_correlation_from_causation,
  preserve_uncertainty
 ]
}

VALIDATE {
 REQUIRE DigestiveSystem
 REQUIRE GastrointestinalTract
 REQUIRE Stomach
 REQUIRE SmallIntestine
 REQUIRE LargeIntestine
 REQUIRE Pancreas
 REQUIRE Liver
 REQUIRE Digestion
 REQUIRE NutrientAbsorption
 REQUIRE GastrointestinalMotility
 REQUIRE EntericNervousSystem
 REQUIRE GastrointestinalHormone
 REQUIRE GutMicrobiota
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT MechanicalDigestion != ChemicalDigestion
 ASSERT Digestion != NutrientAbsorption
 ASSERT luminal_concentration != absorbed_flux
 ASSERT microbial_association != causal_effect
 ASSERT correlation != causal_relationship
}

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 "DigestiveSystemOntology"