Metabolism Ontology

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

flow "MetabolismOntology" v1.0

ENTITY MetabolismOntology {
 TYPE: BiologicalOntology
 DOMAIN: Biochemistry
 SUBJECT: Metabolism
 PURPOSE: FormalSemanticRepresentation
}

PAGE {
 TITLE: "Metabolism Ontology"
 PARENT_DOMAIN: "Biochemistry"
 CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/biochemistry/metabolism-ontology.html"
 AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY Metabolism {
 IS_A: BiochemicalSystem
 COMPOSED_OF: MetabolicPathways
 INCLUDES: [Catabolism, Anabolism]
}

ENTITY MetabolicPathway {
 COMPOSED_OF: OrderedBiochemicalReactions
 HAS: [Inputs, Intermediates, Outputs]
 MAY_BE: [Linear, Branched, Cyclic]
}

ENTITY MetabolicReaction {
 CONVERTS: Metabolite
 TO: Metabolite
 MAY_BE_CATALYSED_BY: Enzyme
}

ENTITY Metabolite {
 MAY_BE: [Substrate, Intermediate, Product, Cofactor]
 PARTICIPATES_IN: MetabolicReaction
}

PROCESS Catabolism {
 BREAKS_DOWN: Molecules
 MAY_RELEASE: UsableEnergy
 MAY_PRODUCE: [ATP, NADH, FADH2]
}

PROCESS Anabolism {
 BUILDS: ComplexMolecules
 FROM: Precursors
 REQUIRES: [Energy, ReducingPower]
}

ENTITY ATP { FUNCTIONS_AS: CellularEnergyCarrier }
ENTITY NADH { IS_A: ReducedElectronCarrier }
ENTITY NADPH { OFTEN_SUPPORTS: ReductiveBiosynthesis }
ENTITY FADH2 { IS_A: ReducedElectronCarrier }

ENTITY GibbsFreeEnergy {
 SYMBOL: DeltaG
 DESCRIBES: ThermodynamicDrivingPotential
}

RULE ReactionDirectionRule {
 IF DeltaG < 0
 THEN forward_reaction IS_THERMODYNAMICALLY_FAVOURABLE
 UNDER defined_conditions
}

ENTITY MetabolicFlux {
 DESCRIBES: RateOfMaterialFlowThroughPathway
 DEPENDS_ON: [EnzymeActivity, SubstrateAvailability, ProductConcentration, CofactorAvailability, Transport, Regulation]
}

RULE FluxConstraint {
 MetabolicFlux != MetaboliteConcentration
}

PROCESS Glycolysis {
 INPUT: Glucose
 OUTPUT: Pyruvate
 PRODUCES: [ATP, NADH]
}

PROCESS Gluconeogenesis {
 PRODUCES: Glucose
 FROM: NonCarbohydratePrecursors
 REQUIRES: Energy
}

RULE GlycolysisGluconeogenesisDistinction {
 Glycolysis != simple_reverse_of_Gluconeogenesis
}

PROCESS Glycogenesis {
 SYNTHESIZES: Glycogen
 FROM: ActivatedGlucosePrecursors
}

PROCESS Glycogenolysis {
 DEGRADES: Glycogen
 PRODUCES: GlucoseDerivedIntermediates
}

PROCESS PentosePhosphatePathway {
 PRODUCES: [NADPH, PentosePhosphates]
}

ENTITY AcetylCoA {
 IS_A: CentralMetabolicIntermediate
 CONNECTS: [CarbohydrateMetabolism, LipidMetabolism, AminoAcidMetabolism, CitricAcidCycle]
}

PROCESS PyruvateOxidation {
 CONVERTS: Pyruvate
 TO: AcetylCoA
 PRODUCES: NADH
}

PROCESS CitricAcidCycle {
 OXIDIZES: AcetylCoA
 PRODUCES: [NADH, FADH2, GTPOrATP, CarbonDioxide]
}

PROCESS ElectronTransportChain {
 TRANSFERS: Electrons
 FROM: ReducedElectronCarriers
 MAY_GENERATE: ProtonMotiveForce
}

ENTITY ProtonMotiveForce {
 STORES: ElectrochemicalPotentialEnergy
 MAY_DRIVE: ATPProduction
}

PROCESS OxidativePhosphorylation {
 USES: ProtonMotiveForce
 PRODUCES: ATP
 CATALYSED_IN_PART_BY: ATPSynthase
}

ENTITY ATPSynthase {
 IS_A: EnzymeComplex
 CATALYSES: ATPFormation
 COUPLED_TO: ProtonFlow
}

PROCESS Fermentation {
 REGENERATES: OxidizedElectronCarrier
 MAY_SUPPORT: ContinuedGlycolysis
}

PROCESS BetaOxidation {
 DEGRADES: FattyAcylCoA
 PRODUCES: [AcetylCoA, NADH, FADH2]
}

PROCESS FattyAcidSynthesis {
 SYNTHESIZES: FattyAcid
 USES: [AcetylDerivedPrecursors, NADPH]
}

PROCESS AminoAcidMetabolism {
 INCLUDES: [AminoAcidBiosynthesis, AminoAcidDegradation, Transamination, Deamination]
}

PROCESS Transamination {
 TRANSFERS: AminoGroup
 BETWEEN: AminoAcidAndKetoAcid
}

PROCESS NitrogenMetabolism {
 MAY_INCLUDE: [AminoAcidMetabolism, UreaCycle, NitrogenAssimilation]
}

PROCESS NucleotideMetabolism {
 INCLUDES: [NucleotideBiosynthesis, NucleotideDegradation, SalvagePathway]
}

PROCESS MetabolicRegulation {
 MODULATES: MetabolicFlux
 MAY_USE: [AllostericRegulation, CovalentModification, SubstrateAvailability, EnzymeExpression, Compartmentalization]
}

PROCESS FeedbackInhibition {
 OCCURS_WHEN: DownstreamProductInhibitsUpstreamStep
}

ENTITY AllostericRegulator {
 BINDS: RegulatorySite
 MAY_CHANGE: EnzymeActivity
}

ENTITY MetabolicCompartment {
 MAY_BE: [Cytosol, Mitochondrion, Peroxisome, Chloroplast, EndoplasmicReticulum]
}

PROCESS MetaboliteTransport {
 MOVES: Metabolite
 ACROSS: MembraneOrCompartmentBoundary
 MAY_USE: Transporter
}

ENTITY MetabolicNetwork {
 NODES: [Metabolites, Reactions]
 EDGES: BiochemicalTransformations
}

ENTITY MetabolicHomeostasis {
 MAINTAINS: MetaboliteAndEnergyBalance
 THROUGH: Regulation
}

ENTITY MetabolicState {
 DESCRIBES: IntegratedMetabolicCondition
 MAY_DEPEND_ON: [NutrientAvailability, EnergyDemand, HormonalSignals, OxygenAvailability, CellType]
}

PROCESS Metabolomics {
 MEASURES: Metabolites
 WITHIN: BiologicalSample
 MAY_USE: [MassSpectrometry, NuclearMagneticResonance, Chromatography]
}

ENTITY Metabolome {
 REPRESENTS: CollectionOfMetabolites
 WITHIN: DefinedBiologicalContext
}

ENTITY MetaboliteAbundance {
 DESCRIBES: AmountOfMetabolite
 IN: DefinedSampleOrCompartment
}

RULE AbundanceFluxDistinction {
 MetaboliteAbundance != MetabolicFlux
}

PROCESS IsotopeTracing {
 USES: IsotopicallyLabelledSubstrate
 TRACKS: AtomFlowThroughMetabolism
 MAY_INFORM: MetabolicFlux
}

ENTITY StoichiometricModel {
 REPRESENTS: MetabolicNetwork
 USING: ReactionStoichiometry
}

PROCESS FluxBalanceAnalysis {
 ABBREVIATION: FBA
 USES: StoichiometricModel
 ESTIMATES: FeasibleFluxDistribution
 SUBJECT_TO: ConstraintsAndObjective
}

RULE FBADistinction {
 FBA_prediction != direct_flux_measurement
}

ENTITY Evidence {
 TYPES: [BiochemicalEvidence, MetabolomicEvidence, FluxomicEvidence, IsotopeTracingEvidence, EnzymaticEvidence, ProteomicEvidence, GeneticEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_metabolic_models
  RECORD organism
  RECORD cell_type
  RECORD compartment
  RECORD nutrient_state
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION Metabolism COMPOSED_OF MetabolicPathway
RELATION MetabolicPathway COMPOSED_OF MetabolicReaction
RELATION Metabolite PARTICIPATES_IN MetabolicReaction
RELATION Enzyme CATALYSES MetabolicReaction
RELATION Catabolism PART_OF Metabolism
RELATION Anabolism PART_OF Metabolism
RELATION MetabolicRegulation MODULATES MetabolicFlux
RELATION MetaboliteTransport CONNECTS MetabolicCompartments
RELATION Metabolome REPRESENTS MetabolicState

SEMANTIC_EQUIVALENCE {
 "metabolism" ~= "integrated biochemical transformation network"
 "metabolic pathway" ~= "biochemical pathway" WHEN metabolism_context
 "metabolic flux" ~= "rate of metabolic pathway flow" WHEN quantitative_context
 "metabolome" ~= "collection of metabolites in a defined biological context"
 "FBA" ~= "flux balance analysis"
}

CONFIDENCE MetabolismAssertion {
 INPUTS: [biochemical_support, metabolomic_support, flux_support, isotope_tracing_support, enzyme_support, experimental_quality, replication, source_independence, contextual_consistency, 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 PathwayInference {
 IF ReactionA produces MetaboliteX
 AND ReactionB consumes MetaboliteX
 THEN metabolic_connection MAY_BE_SUPPORTED
}

RULE FluxInference {
 IF isotope_tracing_and_mass_balance_data ARE_AVAILABLE
 THEN MetabolicFlux MAY_BE_ESTIMATED
 WITH model_and_uncertainty
}

RULE RegulationInference {
 IF perturbation_of_regulator reproducibly_changes pathway_flux
 THEN regulatory_relationship MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF metabolite_abundance correlates_with biological_state
 THEN DO_NOT_INFER causal_metabolic_role
 WITHOUT functional_or_interventional_evidence
}

QUERY MetabolismLookup(context_identifier) {
 RETURN [metabolic_state, pathways, metabolites, reactions, enzymes, compartments, energy_carriers, fluxes, regulation, transport, evidence, confidence]
}

QUERY MetabolicPathwayLookup(pathway_identifier) {
 RETURN [inputs, reactions, enzymes, intermediates, outputs, stoichiometry, energy_balance, flux, regulation, compartments, evidence, confidence]
}

QUERY MetaboliteLookup(metabolite_identifier) {
 RETURN [identity, producing_reactions, consuming_reactions, pathways, compartments, abundance, transport, isotopologues, evidence, confidence]
}

UPDATE_MODEL {
 ON new_metabolic_evidence:
  validate_provenance()
  identify_organism_cell_type_and_compartment()
  normalize_metabolite_identifiers()
  normalize_reaction_and_enzyme_identifiers()
  validate_stoichiometry_and_directionality()
  capture_nutrient_energy_and_oxygen_state()
  capture_timepoint_and_measurement_method()
  map_pathway_connectivity()
  estimate_or_update_flux_when_supported()
  compare_existing_metabolic_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_metabolic_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [metabolic_state, metabolite_identity, reaction_identity, pathway_context, stoichiometry, compartment, flux, regulation, measurement_method, evidence_provenance, confidence]
 REQUIREMENTS: [distinguish_catabolism_from_anabolism, preserve_reaction_direction, preserve_compartment, preserve_species_and_cell_type_context, preserve_nutrient_and_energy_state, distinguish_metabolite_abundance_from_flux, distinguish_thermodynamics_from_kinetics, distinguish_model_prediction_from_direct_measurement, distinguish_association_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE Metabolism
 REQUIRE MetabolicPathway
 REQUIRE MetabolicReaction
 REQUIRE Metabolite
 REQUIRE Catabolism
 REQUIRE Anabolism
 REQUIRE MetabolicFlux
 REQUIRE Glycolysis
 REQUIRE CitricAcidCycle
 REQUIRE OxidativePhosphorylation
 REQUIRE MetabolicRegulation
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT Catabolism != Anabolism
 ASSERT MetaboliteAbundance != MetabolicFlux
 ASSERT FBA_prediction != direct_flux_measurement
 ASSERT thermodynamic_favourability != reaction_rate
 ASSERT correlation != causal_metabolic_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 "MetabolismOntology"