ATP Ontology

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

flow "ATPOntology" v1.0

ENTITY ATPOntology {
 TYPE: BiologicalOntology
 DOMAIN: Biochemistry
 SUBJECT: ATP
 PURPOSE: FormalSemanticRepresentation
}

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

# ============================================================
# CORE MODEL
# ============================================================

ENTITY ATP {
 FULL_NAME: AdenosineTriphosphate
 IS_A: NucleotideTriphosphate
 FUNCTIONS_AS: CellularEnergyCarrier
 COMPOSED_OF: [Adenine, Ribose, ThreePhosphateGroups]
 PARTICIPATES_IN: [EnergyTransfer, Phosphorylation, Biosynthesis, Transport, MechanicalWork]
}

ENTITY Adenosine {
 COMPOSED_OF: [Adenine, Ribose]
 PART_OF: ATP
}

ENTITY PhosphateGroup {
 PART_OF: ATP
 PARTICIPATES_IN: PhosphorylTransfer
}

ENTITY NucleotideTriphosphate {
 IS_A: Nucleotide
 HAS: ThreePhosphateGroups
}

# ============================================================
# ATP / ADP / AMP SYSTEM
# ============================================================

ENTITY ADP {
 FULL_NAME: AdenosineDiphosphate
 HAS: TwoPhosphateGroups
 MAY_BE_PHOSPHORYLATED_TO: ATP
}

ENTITY AMP {
 FULL_NAME: AdenosineMonophosphate
 HAS: OnePhosphateGroup
}

RELATION ATP MAY_BE_CONVERTED_TO ADP
RELATION ADP MAY_BE_CONVERTED_TO ATP
RELATION ADP MAY_BE_CONVERTED_TO AMP

# ============================================================
# ATP HYDROLYSIS
# ============================================================

PROCESS ATPHydrolysis {
 INPUT: ATP
 MAY_PRODUCE: [ADPPlusPi, AMPPlusPPi]
 IS_EXERGONIC_UNDER: TypicalCellularConditions
 MAY_DRIVE: CoupledProcess
}

ENTITY InorganicPhosphate {
 SYMBOL: Pi
 MAY_BE_PRODUCT_OF: ATPHydrolysis
}

ENTITY Pyrophosphate {
 SYMBOL: PPi
 MAY_BE_PRODUCT_OF: ATPToAMPReaction
}

RULE ATPHydrolysisRule {
 IF ATP -> ADP + Pi
 THEN free_energy_change := condition_dependent
 AND energy_may_be_coupled_to cellular_work
}

RULE EnergyLanguageConstraint {
 ATP DOES_NOT_CONTAIN abstract_free_energy_as_a_substance
 ATP_hydrolysis HAS thermodynamic_free_energy_change
 UNDER defined_conditions
}

# ============================================================
# PHOSPHORYL TRANSFER
# ============================================================

PROCESS PhosphorylTransfer {
 TRANSFERS: PhosphorylGroup
 FROM: Donor
 TO: Acceptor
}

PROCESS ATPDependentPhosphorylation {
 DONOR: ATP
 ACCEPTOR: Substrate
 MAY_PRODUCE: ADP
}

ENTITY Kinase {
 IS_A: Enzyme
 CATALYSES: PhosphorylTransfer
}

RULE KinaseRule {
 IF Kinase uses ATP_as_phosphoryl_donor
 THEN substrate_phosphorylation MAY_OCCUR
}

# ============================================================
# ENERGY COUPLING
# ============================================================

PROCESS EnergyCoupling {
 LINKS: ExergonicProcess
 TO: EndergonicProcess
 MAY_USE: ATPHydrolysis
}

RULE CoupledReactionRule {
 DeltaG_total := sum(DeltaG_component_reactions)
 IF DeltaG_total < 0
 THEN coupled_process MAY_BE thermodynamically_favourable
}

RULE CouplingConstraint {
 ATP_hydrolysis_occurrence != proof_of_effective_coupling
 WITHOUT mechanistic_connection
}

# ============================================================
# ATP SYNTHESIS
# ============================================================

PROCESS ATPSynthesis {
 INPUTS: [ADP, InorganicPhosphate]
 OUTPUT: ATP
 REQUIRES: EnergyInput
}

ENTITY ATPSynthase {
 IS_A: EnzymeComplex
 CATALYSES: ATPSynthesis
 MAY_USE: ProtonMotiveForce
}

PROCESS OxidativePhosphorylation {
 PRODUCES: ATP
 THROUGH: [ElectronTransport, ProtonMotiveForce, ATPSynthase]
}

PROCESS Photophosphorylation {
 PRODUCES: ATP
 USING: LightDrivenElectronTransport
 IN: PhotosyntheticSystems
}

PROCESS SubstrateLevelPhosphorylation {
 PRODUCES: ATP
 BY: DirectPhosphorylTransferToADP
}

# ============================================================
# PROTON MOTIVE FORCE
# ============================================================

ENTITY ProtonMotiveForce {
 IS_A: ElectrochemicalPotential
 ACROSS: Membrane
 MAY_DRIVE: ATPSynthase
}

ENTITY ProtonGradient {
 CONTRIBUTES_TO: ProtonMotiveForce
}

ENTITY MembranePotential {
 CONTRIBUTES_TO: ProtonMotiveForce
}

RULE ChemiosmoticCoupling {
 IF ProtonMotiveForce drives_proton_flow_through ATPSynthase
 THEN ATPSynthesis MAY_OCCUR
}

# ============================================================
# CELLULAR RESPIRATION
# ============================================================

PROCESS CellularRespiration {
 OXIDIZES: MetabolicFuel
 MAY_PRODUCE: ATP
 INCLUDES: [Glycolysis, CitricAcidCycle, OxidativePhosphorylation]
}

PROCESS Glycolysis {
 MAY_PRODUCE: ATP
 THROUGH: SubstrateLevelPhosphorylation
}

PROCESS CitricAcidCycle {
 PRODUCES: ReducedElectronCarriers
 MAY_PRODUCE: GTPOrATP
}

PROCESS ElectronTransportChain {
 TRANSFERS: Electrons
 MAY_GENERATE: ProtonMotiveForce
}

# ============================================================
# ATP IN BIOSYNTHESIS
# ============================================================

PROCESS ATPDependentBiosynthesis {
 USES: ATP
 TO_DRIVE: EndergonicBiosyntheticSteps
}

ENTITY ActivatedIntermediate {
 MAY_BE_GENERATED_BY: ATPDependentReaction
 HAS: IncreasedReactionPotential
}

RULE BiosyntheticCouplingRule {
 IF biosynthetic_step requires_activation
 THEN ATP MAY_BE_USED_TO_FORM activated_intermediate
}

# ============================================================
# ATP IN ACTIVE TRANSPORT
# ============================================================

PROCESS ATPDrivenTransport {
 SUBCLASS_OF: ActiveTransport
 USES: ATPHydrolysis
 MOVES: SoluteAcrossMembrane
}

ENTITY ATPasePump {
 IS_A: MembraneProtein
 HYDROLYSES: ATP
 COUPLES_TO: SoluteTransport
}

RULE TransportCouplingRule {
 IF ATPasePump hydrolyses_ATP
 AND conformational_cycle_moves_solute
 THEN ATPHydrolysis IS_COUPLED_TO transport
}

# ============================================================
# ATP IN MECHANICAL WORK
# ============================================================

PROCESS ATPDrivenMechanicalWork {
 USES: ATPHydrolysis
 MAY_POWER: MolecularMotor
}

ENTITY MolecularMotor {
 IS_A: Protein
 CONVERTS: ChemicalEnergy
 TO: MechanicalWork
}

ENTITY MotorATPase {
 SUBCLASS_OF: ATPase
 PARTICIPATES_IN: MechanicalWork
}

# ============================================================
# ATPASES
# ============================================================

ENTITY ATPase {
 IS_A: Enzyme
 CATALYSES: ATPHydrolysis
}

ENTITY ATPaseActivity {
 DESCRIBES: RateOfATPHydrolysis
 UNDER: DefinedConditions
}

RULE ATPaseActivityConstraint {
 ATP_binding != ATP_hydrolysis
 ATP_hydrolysis != productive_energy_coupling
}

# ============================================================
# ATP BINDING
# ============================================================

ENTITY ATPBindingProtein {
 IS_A: Protein
 BINDS: ATP
}

ENTITY ATPBindingSite {
 PART_OF: ATPBindingProtein
 INTERACTS_WITH: ATP
}

RULE BindingFunctionConstraint {
 ATP_binding DOES_NOT_BY_ITSELF imply ATPase_activity
}

# ============================================================
# ATP IN SIGNAL TRANSDUCTION
# ============================================================

PROCESS ATPDependentSignalTransduction {
 MAY_USE: ProteinKinase
 MAY_CHANGE: ProteinPhosphorylationState
}

ENTITY ProteinKinase {
 SUBCLASS_OF: Kinase
 PHOSPHORYLATES: Protein
 MAY_USE: ATP
}

RELATION ATP PARTICIPATES_IN ProteinPhosphorylation

# ============================================================
# ATP IN NUCLEIC ACID PROCESSES
# ============================================================

PROCESS ATPDependentNucleicAcidProcess {
 MAY_INCLUDE: [HelicaseActivity, ChromatinRemodelling, Ligation, Transport]
}

ENTITY ATPDependentHelicase {
 IS_A: Enzyme
 USES: ATP
 MAY_UNWIND: NucleicAcid
}

RULE NucleicAcidEnergyRule {
 IF ATPDependentEnzyme couples_ATP_hydrolysis_to_nucleic_acid_rearrangement
 THEN chemical_energy MAY_DRIVE conformational_or_mechanical_change
}

# ============================================================
# ATP HOMEOSTASIS
# ============================================================

ENTITY ATPHomeostasis {
 BALANCES: [ATPSynthesis, ATPConsumption]
 MAINTAINS: CellularEnergyState
}

ENTITY ATPConcentration {
 DESCRIBES: ATPAmountPerDefinedVolumeOrCompartment
}

ENTITY ATP_ADP_Ratio {
 RELATES: ATPAbundance
 TO: ADPAbundance
 MAY_REFLECT: CellularEnergyState
}

ENTITY AdenylateEnergyCharge {
 DESCRIBES: RelativeStateOfAdenineNucleotidePool
 USES: [ATP, ADP, AMP]
}

RULE EnergyChargeRule {
 AdenylateEnergyCharge :=
  (ATP + 0.5 * ADP) / (ATP + ADP + AMP)
 WHEN denominator > 0
}

# ============================================================
# ADENYLATE KINASE
# ============================================================

PROCESS AdenylateKinaseReaction {
 CONVERTS: [TwoADP]
 TO: [ATP, AMP]
 REVERSIBLE: true
}

ENTITY AdenylateKinase {
 IS_A: Enzyme
 CATALYSES: AdenylateKinaseReaction
}

RULE AdenylateBalanceRule {
 adenine_nucleotide_interconversion MAY_BUFFER cellular_energy_state
}

# ============================================================
# ATP TURNOVER
# ============================================================

ENTITY ATPTurnover {
 DESCRIBES: ContinuousSynthesisAndConsumptionOfATP
}

RULE TurnoverRule {
 ATP_pool_size != total_ATP_flux
}

RULE SteadyStateRule {
 IF ATP_concentration approximately_constant
 THEN synthesis_rate MAY_APPROXIMATE consumption_rate
 BUT high_turnover MAY_STILL_OCCUR
}

# ============================================================
# COMPARTMENTALIZATION
# ============================================================

ENTITY ATPCompartment {
 MAY_BE: [Cytosol, Mitochondrion, Chloroplast, Nucleus]
}

RELATION ATP LOCATED_IN ATPCompartment

PROCESS ATPTransport {
 MOVES: AdenineNucleotide
 BETWEEN: Compartments
 MAY_USE: NucleotideTransporter
}

RULE CompartmentConstraint {
 ATP_measurement MUST_PRESERVE compartment_context
 WHEN compartment_specific_interpretation_is_required
}

# ============================================================
# METABOLIC REGULATION
# ============================================================

ENTITY EnergySensor {
 RESPONDS_TO: CellularEnergyState
 MAY_BE_INFLUENCED_BY: [ATP, ADP, AMP]
}

RULE EnergySensingRule {
 changes_in_adenine_nucleotide_state MAY_MODULATE metabolic_regulation
 THROUGH defined_energy_sensing_mechanisms
}

# ============================================================
# ATP MEASUREMENT
# ============================================================

PROCESS ATPMeasurement {
 MEASURES: ATP
 MAY_USE: [LuminescenceAssay, Chromatography, MassSpectrometry, Spectroscopy]
}

ENTITY ATPMeasurementResult {
 HAS: [Value, Unit, Sample, Compartment, Method, Timepoint]
}

RULE MeasurementContextRule {
 IF ATP_values ARE_COMPARED
 THEN preserve [
  sample_type,
  compartment,
  normalization_method,
  assay_method,
  timepoint
 ]
}

# ============================================================
# EVIDENCE
# ============================================================

ENTITY Evidence {
 TYPES: [
  BiochemicalEvidence,
  BioenergeticEvidence,
  EnzymaticEvidence,
  MetabolomicEvidence,
  StructuralEvidence,
  TransportEvidence,
  ExperimentalEvidence,
  ComputationalEvidence,
  LiteratureEvidence
 ]
}

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_assertions
  RECORD ATP_context
  RECORD cellular_compartment
  RECORD metabolic_state
  RECORD assay_method
  RECORD temperature_and_pH
  RECORD provenance
  REDUCE confidence
 }
}

# ============================================================
# SEMANTIC RELATIONSHIPS
# ============================================================

RELATION ATP IS_A NucleotideTriphosphate
RELATION ATP MAY_BE_HYDROLYSED_TO ADP
RELATION ATPHydrolysis MAY_DRIVE EnergyCoupling
RELATION ATPSynthase CATALYSES ATPSynthesis
RELATION ProtonMotiveForce MAY_DRIVE ATPSynthase
RELATION ATPase CATALYSES ATPHydrolysis
RELATION ProteinKinase MAY_USE ATP
RELATION ATP PARTICIPATES_IN CellularMetabolism
RELATION ATPHomeostasis BALANCES SynthesisAndConsumption

# ============================================================
# SEMANTIC EQUIVALENCE
# ============================================================

SEMANTIC_EQUIVALENCE {
 "ATP" ~= "adenosine triphosphate"
 "ADP" ~= "adenosine diphosphate"
 "AMP" ~= "adenosine monophosphate"
 "ATP hydrolysis" ~= "hydrolysis of adenosine triphosphate"
 "ATP synthase" ~= "adenosine triphosphate synthase"
}

RULE EquivalenceConstraint {
 IF terms ARE semantic_equivalents
 THEN preserve_chemical_identity()
 AND preserve_reaction_direction()
 AND preserve_compartment()
 AND preserve_metabolic_state()
 AND preserve_experimental_conditions()
 AND prevent_false_identity()
}

# ============================================================
# CONFIDENCE MODEL
# ============================================================

CONFIDENCE ATPAssertion {
 INPUTS: [
  biochemical_support,
  thermodynamic_support,
  enzymatic_support,
  bioenergetic_support,
  structural_support,
  measurement_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"
}

# ============================================================
# REASONING RULES
# ============================================================

RULE ATPProductionInference {
 IF ADP_and_Pi are_converted_to_ATP
 AND energy_source_is_identified
 THEN ATPSynthesis MAY_BE_SUPPORTED
}

RULE ATPConsumptionInference {
 IF ATP decreases_while_ADP_or_AMP_products_increase
 AND enzyme_or_process_is_supported
 THEN ATPConsumption MAY_BE_INFERRED
}

RULE CouplingInference {
 IF ATPHydrolysis and endergonic_process are_mechanistically_linked
 THEN EnergyCoupling MAY_BE_SUPPORTED
}

RULE EnergyStateInference {
 IF ATP_ADP_AMP concentrations ARE_KNOWN
 THEN adenylate_energy_charge MAY_BE_CALCULATED
}

RULE CausalityConstraint {
 IF ATP_level correlates_with cellular_state
 THEN DO_NOT_INFER causal_mechanism
 WITHOUT functional_or_interventional_evidence
}

# ============================================================
# QUERY MODEL
# ============================================================

QUERY ATPLookup(context_identifier) {
 RETURN [
  chemical_identity,
  concentration,
  compartment,
  ATP_ADP_ratio,
  adenylate_energy_charge,
  synthesis_processes,
  consumption_processes,
  coupled_reactions,
  enzymes,
  metabolic_state,
  evidence,
  confidence
 ]
}

QUERY ATPReactionLookup(reaction_identifier) {
 RETURN [
  ATP_role,
  substrates,
  products,
  enzyme,
  stoichiometry,
  thermodynamics,
  coupling_mechanism,
  compartment,
  evidence,
  confidence
 ]
}

QUERY ATPHomeostasisLookup(context_identifier) {
 RETURN [
  ATP_pool,
  ADP_pool,
  AMP_pool,
  synthesis_rate,
  consumption_rate,
  turnover,
  energy_charge,
  compartments,
  regulation,
  evidence,
  confidence
 ]
}

# ============================================================
# UPDATE MODEL
# ============================================================

UPDATE_MODEL {
 ON new_ATP_evidence:
  validate_provenance()
  identify_organism_cell_type_and_compartment()
  normalize_ATP_ADP_AMP_identifiers()
  normalize_reaction_identifiers()
  capture_temperature_pH_and_metabolic_state()
  map_ATP_synthesis_and_consumption()
  map_energy_coupling_relationships()
  capture_measurement_method_and_timepoint()
  calculate_energy_charge_when_supported()
  compare_existing_assertions()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_ATP_relationships()
  update_flow_hash()
}

# ============================================================
# AI CONSUMPTION
# ============================================================

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [
  ATP_identity,
  ATP_ADP_AMP_state,
  reaction_direction,
  synthesis_or_consumption,
  energy_coupling,
  compartment,
  metabolic_state,
  thermodynamic_context,
  measurement_method,
  evidence_provenance,
  confidence
 ]
 REQUIREMENTS: [
  preserve_chemical_identity,
  preserve_reaction_direction,
  preserve_cellular_compartment,
  preserve_metabolic_state,
  distinguish_ATP_pool_from_ATP_flux,
  distinguish_ATP_binding_from_ATP_hydrolysis,
  distinguish_ATP_hydrolysis_from_productive_coupling,
  distinguish_thermodynamics_from_kinetics,
  distinguish_correlation_from_causation,
  preserve_experimental_conditions
 ]
}

# ============================================================
# VALIDATION
# ============================================================

VALIDATE {
 REQUIRE ATP
 REQUIRE ADP
 REQUIRE AMP
 REQUIRE ATPHydrolysis
 REQUIRE ATPSynthesis
 REQUIRE ATPSynthase
 REQUIRE EnergyCoupling
 REQUIRE ATPase
 REQUIRE ATPHomeostasis
 REQUIRE AdenylateEnergyCharge
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT ATP != ADP
 ASSERT ATP_binding != ATP_hydrolysis
 ASSERT ATP_hydrolysis != productive_energy_coupling
 ASSERT ATP_pool_size != ATP_flux
 ASSERT thermodynamic_favourability != reaction_rate
}

# ============================================================
# FLOW HASH
# ============================================================

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 "ATPOntology"