Metabolic Pathway Ontology

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

flow "MetabolicPathwayOntology" v1.0

ENTITY MetabolicPathwayOntology {
 TYPE: BiologicalOntology
 DOMAIN: Biochemistry
 SUBJECT: MetabolicPathway
 PURPOSE: FormalSemanticRepresentation
}

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

ENTITY MetabolicPathway {
 IS_A: BiochemicalPathway
 COMPOSED_OF: OrderedMetabolicReactions
 HAS: [Inputs, Intermediates, Outputs]
 MAY_BE: [LinearPathway, BranchedPathway, CyclicPathway]
 OCCURS_IN: BiologicalContext
}

ENTITY MetabolicReaction {
 CONVERTS: Substrate
 TO: Product
 MAY_BE_CATALYSED_BY: Enzyme
}

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

ENTITY Enzyme {
 CATALYSES: MetabolicReaction
 MAY_BE_REGULATED_BY: MetabolicRegulation
}

RULE PathwayContinuity {
 IF ReactionA produces MetaboliteX
 AND ReactionB consumes MetaboliteX
 THEN ReactionA MAY_PRECEDE ReactionB
 IN compatible_context
}

ENTITY LinearPathway {
 SUBCLASS_OF: MetabolicPathway
 HAS: SequentialReactionFlow
}

ENTITY BranchedPathway {
 SUBCLASS_OF: MetabolicPathway
 HAS: BranchPoint
}

ENTITY CyclicPathway {
 SUBCLASS_OF: MetabolicPathway
 REGENERATES: CycleIntermediate
}

ENTITY BranchPoint {
 MAY_DISTRIBUTE: MetabolicFlux
 BETWEEN: AlternativeReactions
}

ENTITY CatabolicPathway {
 SUBCLASS_OF: MetabolicPathway
 DEGRADES: Molecules
 MAY_CAPTURE: ChemicalEnergy
}

ENTITY AnabolicPathway {
 SUBCLASS_OF: MetabolicPathway
 SYNTHESIZES: ComplexMolecules
 REQUIRES: Precursors
 MAY_REQUIRE: [ATP, NADPH]
}

ENTITY AmphibolicPathway {
 SUBCLASS_OF: MetabolicPathway
 PARTICIPATES_IN: [Catabolism, Anabolism]
}

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

PROCESS BetaOxidation {
 SUBCLASS_OF: CatabolicPathway
 INPUT: FattyAcylCoA
 PRODUCES: [AcetylCoA, NADH, FADH2]
}

PROCESS FattyAcidSynthesis {
 SUBCLASS_OF: AnabolicPathway
 PRODUCES: FattyAcid
 USES: [AcetylDerivedPrecursors, NADPH]
}

PROCESS Gluconeogenesis {
 SUBCLASS_OF: AnabolicPathway
 PRODUCES: Glucose
 FROM: NonCarbohydratePrecursors
}

PROCESS CitricAcidCycle {
 SUBCLASS_OF: AmphibolicPathway
 OXIDIZES: AcetylCoA
 PRODUCES: [NADH, FADH2, GTPOrATP, CarbonDioxide]
 PROVIDES: BiosyntheticIntermediates
}

ENTITY PathwayInput {
 ENTERS: MetabolicPathway
}

ENTITY PathwayOutput {
 EXITS_OR_ACCUMULATES_FROM: MetabolicPathway
 MAY_FEED: AnotherPathway
}

ENTITY MetabolicIntermediate {
 IS_PRODUCT_OF: UpstreamReaction
 IS_SUBSTRATE_OF: DownstreamReaction
}

ENTITY ReactionStoichiometry {
 DESCRIBES: QuantitativeReactantProductRelationship
}

ENTITY PathwayStoichiometry {
 AGGREGATES: ReactionStoichiometry
 ACROSS: MetabolicPathway
}

RULE MassBalanceRule {
 IF pathway_boundary_and_reactions ARE_DEFINED
 THEN conserved_atoms SHOULD_BALANCE
 SUBJECT_TO exchange_and_pool_assumptions
}

ENTITY ReactionFreeEnergy {
 SYMBOL: DeltaG
 DESCRIBES: ThermodynamicDrivingPotential
}

RULE PathwayThermodynamics {
 DeltaG_pathway := sum(DeltaG_component_reactions)
 UNDER compatible_conditions
}

RULE ThermodynamicConstraint {
 favourable_DeltaG != high_flux
}

ENTITY MetabolicFlux {
 DESCRIBES: RateOfMaterialFlow
 THROUGH: MetabolicPathway
}

RULE FluxDependence {
 MetabolicFlux MAY_DEPEND_ON [
  enzyme_activity,
  substrate_supply,
  product_removal,
  cofactor_availability,
  transport,
  regulation,
  compartment
 ]
}

RULE ConcentrationFluxDistinction {
 metabolite_concentration != pathway_flux
}

PROCESS PathwayRegulation {
 MODULATES: MetabolicFlux
 MAY_USE: [
  AllostericRegulation,
  CovalentModification,
  FeedbackInhibition,
  FeedforwardActivation,
  EnzymeExpression,
  SubstrateAvailability
 ]
}

PROCESS FeedbackInhibition {
 OCCURS_WHEN: DownstreamProductInhibitsUpstreamReaction
}

PROCESS FeedforwardActivation {
 OCCURS_WHEN: UpstreamSignalOrMetaboliteActivatesDownstreamReaction
}

ENTITY FluxControlCoefficient {
 DESCRIBES: SensitivityOfSystemFluxToComponentActivity
}

RULE DistributedControlRule {
 metabolic_flux_control MAY_BE_DISTRIBUTED_ACROSS multiple_components
}

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

PROCESS IntercompartmentTransport {
 MOVES: Metabolite
 BETWEEN: Compartments
}

RULE CompartmentConstraint {
 IF consecutive_pathway_steps occur_in_different_compartments
 THEN transport_step MAY_BE_REQUIRED
}

PROCESS PathwayCoupling {
 LINKS: MetabolicPathways
 THROUGH: [SharedMetabolite, EnergyCarrier, RedoxCarrier]
}

ENTITY EnergyCarrier {
 MAY_BE: [ATP, GTP]
}

ENTITY RedoxCarrier {
 MAY_BE: [NADH, NADPH, FADH2]
}

ENTITY CentralMetabolism {
 INCLUDES: [Glycolysis, PentosePhosphatePathway, PyruvateMetabolism, CitricAcidCycle, OxidativePhosphorylation]
}

PROCESS PentosePhosphatePathway {
 PRODUCES: [NADPH, PentosePhosphates]
}

PROCESS OxidativePhosphorylation {
 PRODUCES: ATP
 USING: ElectronTransportAndProtonMotiveForce
}

ENTITY MetabolicBranch {
 ORIGINATES_AT: BranchPoint
 LEADS_TO: PathwayDestination
}

PROPERTY ReactionReversibility {
 MAY_BE: [Reversible, EffectivelyIrreversible]
 DEPENDS_ON: ThermodynamicAndCellularConditions
}

ENTITY MetabolicBypass {
 PROVIDES: AlternativeRoute
 AROUND: ReactionOrPathwaySegment
}

ENTITY MetabolicNetwork {
 COMPOSED_OF: InterconnectedMetabolicPathways
 NODES: [Metabolites, Reactions]
}

PROCESS PathwayPerturbation {
 MAY_CHANGE: [EnzymeActivity, MetaboliteLevel, MetabolicFlux]
 MAY_BE: [GeneticPerturbation, ChemicalPerturbation, EnvironmentalPerturbation]
}

PROCESS PathwayMeasurement {
 MAY_MEASURE: [MetaboliteAbundance, EnzymeActivity, ReactionRate, MetabolicFlux, IsotopicEnrichment]
}

PROCESS IsotopeTracing {
 USES: LabelledSubstrate
 TRACKS: AtomFlow
 THROUGH: MetabolicPathway
}

PROCESS Metabolomics {
 MEASURES: MetaboliteAbundance
}

PROCESS Fluxomics {
 ESTIMATES_OR_MEASURES: MetabolicFluxes
}

RULE MeasurementDistinction {
 metabolomics_measurement != direct_flux_measurement
}

ENTITY StoichiometricModel {
 REPRESENTS: MetabolicNetwork
 USING: ReactionStoichiometry
}

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

ENTITY KineticModel {
 REPRESENTS: ReactionDynamics
 USING: KineticParameters
}

RULE ModelPredictionConstraint {
 computational_prediction != direct_experimental_observation
}

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

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_pathway_models
  RECORD organism
  RECORD cell_type
  RECORD compartment
  RECORD metabolic_state
  RECORD reaction_direction
  RECORD measurement_method
  RECORD provenance
  REDUCE confidence
 }
}

RELATION MetabolicPathway COMPOSED_OF MetabolicReaction
RELATION MetabolicReaction CONSUMES Substrate
RELATION MetabolicReaction PRODUCES Product
RELATION Enzyme CATALYSES MetabolicReaction
RELATION MetabolicIntermediate CONNECTS MetabolicReactions
RELATION PathwayRegulation MODULATES MetabolicFlux
RELATION MetabolicPathway OCCURS_IN PathwayCompartment
RELATION MetabolicPathway PART_OF MetabolicNetwork
RELATION PathwayCoupling CONNECTS MetabolicPathways

SEMANTIC_EQUIVALENCE {
 "metabolic pathway" ~= "biochemical pathway" WHEN metabolism_context
 "pathway intermediate" ~= "metabolic intermediate"
 "pathway flux" ~= "metabolic pathway flux"
 "metabolic network" ~= "interconnected biochemical pathway network"
 "FBA" ~= "flux balance analysis"
}

CONFIDENCE MetabolicPathwayAssertion {
 INPUTS: [reaction_support, enzyme_support, stoichiometric_support, metabolomic_support, flux_support, isotope_tracing_support, perturbation_support, 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 PathwayMembershipInference {
 IF Reaction participates_in ordered_transformation_sequence
 AND shares_metabolites_with adjacent_reactions
 THEN Reaction MAY_BE_MEMBER_OF MetabolicPathway
}

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

RULE RegulatoryInference {
 IF regulator_perturbation changes_pathway_flux
 AND effect_is_reproducible
 THEN regulatory_relationship MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF metabolite_abundance correlates_with pathway_activity
 THEN DO_NOT_INFER flux_or_causality
 WITHOUT appropriate_flux_or_interventional_evidence
}

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

QUERY PathwayReactionLookup(pathway_identifier, reaction_identifier) {
 RETURN [substrates, products, enzyme, cofactors, stoichiometry, reversibility, free_energy, flux, regulation, compartment, evidence, confidence]
}

QUERY PathwayNetworkLookup(context_identifier) {
 RETURN [pathways, shared_metabolites, branch_points, coupled_pathways, compartments, flux_distribution, regulatory_links, evidence, confidence]
}

UPDATE_MODEL {
 ON new_metabolic_pathway_evidence:
  validate_provenance()
  identify_organism_cell_type_and_compartment()
  normalize_pathway_metabolite_reaction_and_enzyme_identifiers()
  validate_reaction_stoichiometry()
  determine_reaction_directionality()
  map_pathway_order_and_branching()
  capture_metabolic_state_and_timepoint()
  map_regulatory_and_transport_relationships()
  update_flux_when_supported()
  compare_existing_pathway_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_network_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [pathway_identity, reaction_identity, metabolite_identity, stoichiometry, reaction_direction, enzyme_context, compartment, metabolic_flux, regulation, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_pathway_identity, preserve_reaction_direction, preserve_metabolite_identity, preserve_species_and_cell_type_context, preserve_compartment, distinguish_concentration_from_flux, distinguish_thermodynamics_from_kinetics, distinguish_pathway_membership_from_causal_control, distinguish_model_prediction_from_observation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE MetabolicPathway
 REQUIRE MetabolicReaction
 REQUIRE Metabolite
 REQUIRE Enzyme
 REQUIRE CatabolicPathway
 REQUIRE AnabolicPathway
 REQUIRE AmphibolicPathway
 REQUIRE MetabolicFlux
 REQUIRE PathwayRegulation
 REQUIRE MetabolicNetwork
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT metabolite_concentration != pathway_flux
 ASSERT thermodynamic_favourability != high_flux
 ASSERT pathway_membership != regulatory_control
 ASSERT computational_prediction != direct_observation
 ASSERT correlation != causal_pathway_effect
}

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 "MetabolicPathwayOntology"