Photosynthesis Ontology

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

flow "PhotosynthesisOntology" v1.0

ENTITY PhotosynthesisOntology {
 TYPE: BiologicalOntology
 DOMAIN: Biochemistry
 SUBJECT: Photosynthesis
 PURPOSE: FormalSemanticRepresentation
}

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

PROCESS Photosynthesis {
 IS_A: BioenergeticProcess
 CONVERTS: LightEnergy
 TO: ChemicalEnergy
 MAY_FIX: CarbonDioxide
 PRODUCES: ReducedCarbonCompounds
}

ENTITY PhotosyntheticOrganism {
 MAY_BE: [Plant, Alga, Cyanobacterium, PhotosyntheticBacterium]
 PERFORMS: Photosynthesis
}

PROCESS OxygenicPhotosynthesis {
 SUBCLASS_OF: Photosynthesis
 USES: Water
 PRODUCES: Oxygen
 USES_PHOTOSYSTEMS: [PhotosystemII, PhotosystemI]
}

PROCESS AnoxygenicPhotosynthesis {
 SUBCLASS_OF: Photosynthesis
 DOES_NOT_PRODUCE: OxygenFromWater
 MAY_USE: AlternativeElectronDonor
}

ENTITY Chloroplast {
 IS_A: Organelle
 HOSTS: Photosynthesis
 IN: PlantsAndManyAlgae
}

ENTITY ThylakoidMembrane {
 CONTAINS: [PhotosystemII, CytochromeB6FComplex, PhotosystemI, ATP_Synthase]
 SUPPORTS: LightDependentReactions
}

ENTITY ThylakoidLumen {
 MAY_ACCUMULATE: Protons
}

ENTITY Stroma {
 HOSTS: CarbonFixationReactions
}

ENTITY PhotosyntheticPigment {
 ABSORBS: Light
 MAY_TRANSFER: ExcitationEnergy
}

ENTITY Chlorophyll {
 SUBCLASS_OF: PhotosyntheticPigment
 PARTICIPATES_IN: LightHarvestingAndPhotochemistry
}

ENTITY Carotenoid {
 SUBCLASS_OF: PhotosyntheticPigment
 MAY_FUNCTION_IN: [LightHarvesting, Photoprotection]
}

ENTITY Photosystem {
 IS_A: PigmentProteinComplex
 CONTAINS: [AntennaComplex, ReactionCenter]
}

ENTITY PhotosystemII {
 SUBCLASS_OF: Photosystem
 ABBREVIATION: PSII
 INITIATES: WaterToPlastoquinoneElectronFlow
}

ENTITY PhotosystemI {
 SUBCLASS_OF: Photosystem
 ABBREVIATION: PSI
 CONTRIBUTES_TO: NADPHFormation
}

PROCESS WaterOxidation {
 OCCURS_AT: PhotosystemII
 EXTRACTS: ElectronsFromWater
 PRODUCES: [Protons, Oxygen]
}

ENTITY OxygenEvolvingComplex {
 ASSOCIATED_WITH: PhotosystemII
 CATALYSES: WaterOxidation
}

PROCESS PhotosyntheticElectronTransport {
 TRANSFERS: Electrons
 BETWEEN: PhotosyntheticRedoxComponents
 MAY_GENERATE: ProtonMotiveForce
}

ENTITY Plastoquinone {
 IS_A: ElectronCarrier
 PARTICIPATES_IN: PhotosyntheticElectronTransport
}

ENTITY CytochromeB6FComplex {
 IS_A: ElectronTransferComplex
 CONTRIBUTES_TO: ProtonGradientFormation
}

ENTITY Plastocyanin {
 IS_A: ElectronCarrier
 TRANSFERS_ELECTRONS_TO: PhotosystemI
}

ENTITY Ferredoxin {
 IS_A: ElectronCarrier
 RECEIVES_ELECTRONS_FROM: PhotosystemI
}

ENTITY NADPPlus {
 IS_A: OxidizedElectronCarrier
 MAY_BE_REDUCED_TO: NADPH
}

ENTITY NADPH {
 IS_A: ReducedElectronCarrier
 PROVIDES: ReducingPower
 FOR: CarbonFixationAndBiosynthesis
}

PROCESS Photophosphorylation {
 PRODUCES: ATP
 USING: [LightDrivenElectronTransport, ProtonMotiveForce]
}

ENTITY ProtonMotiveForce {
 IS_A: ElectrochemicalPotential
 ACROSS: ThylakoidMembrane
 MAY_DRIVE: ATP_Synthase
}

ENTITY ATP_Synthase {
 IS_A: EnzymeComplex
 CATALYSES: ATPFormation
 USING: ProtonMotiveForce
}

PROCESS LinearElectronFlow {
 USES: [PhotosystemII, PhotosystemI]
 ELECTRON_SOURCE: Water
 MAY_PRODUCE: [Oxygen, NADPH, ATP]
}

PROCESS CyclicElectronFlow {
 INVOLVES: PhotosystemI
 RETURNS_ELECTRONS_TO: ElectronTransportChain
 MAY_INCREASE: ATPProduction
 DOES_NOT_DIRECTLY_PRODUCE: NADPH
}

PROCESS LightDependentReactions {
 OCCUR_AT: PhotosyntheticMembrane
 REQUIRE: Light
 PRODUCE_OR_SUPPORT: [ATP, NADPH, OxygenInOxygenicSystems]
}

PROCESS CarbonFixation {
 INCORPORATES: InorganicCarbon
 INTO: OrganicMolecule
}

PROCESS CalvinBensonCycle {
 SUBCLASS_OF: CarbonFixationPathway
 USES: [ATP, NADPH, CarbonDioxide]
 PRODUCES: ReducedCarbonIntermediates
 REGENERATES: RuBP
}

ENTITY RuBP {
 FULL_NAME: Ribulose1_5Bisphosphate
 ACCEPTS: CarbonDioxide
}

ENTITY RuBisCO {
 IS_A: Enzyme
 CATALYSES: CarbonDioxideFixationToRuBP
 MAY_ALSO_CATALYSE: OxygenationReaction
}

PROCESS Photorespiration {
 MAY_BEGIN_WITH: RuBisCO_Oxygenation
 CONSUMES: Energy
 MAY_RELEASE: PreviouslyFixedCarbonDioxide
}

PROCESS C3Photosynthesis {
 USES: CalvinBensonCycle
 PRIMARY_INITIAL_CARBON_FIXATION_ENZYME: RuBisCO
}

PROCESS C4Photosynthesis {
 CONCENTRATES: CarbonDioxide
 AROUND: RuBisCO
 USES: SpatialSeparationOfCarbonFixationSteps
 MAY_REDUCE: Photorespiration
}

ENTITY PEP_Carboxylase {
 IS_A: Enzyme
 CATALYSES: InitialCarbonFixationInC4Pathway
}

PROCESS CAMPhotosynthesis {
 FULL_NAME: CrassulaceanAcidMetabolism
 USES: TemporalSeparationOfCarbonFixation
 MAY_SUPPORT: WaterConservation
}

ENTITY AbsorptionSpectrum {
 DESCRIBES: LightAbsorptionByPigment
 ACROSS: Wavelength
}

ENTITY ActionSpectrum {
 DESCRIBES: BiologicalPhotosyntheticEffectiveness
 ACROSS: Wavelength
}

RULE SpectrumDistinction {
 AbsorptionSpectrum != ActionSpectrum
}

ENTITY PhotosyntheticRate {
 DESCRIBES: RateOfPhotosyntheticProcess
 MAY_BE_ESTIMATED_FROM: [CarbonDioxideUptake, OxygenEvolution, ElectronTransport]
}

RULE LimitingFactorRule {
 PhotosyntheticRate MAY_BE_LIMITED_BY [light, carbon_dioxide, temperature, water, nutrient_status, biochemical_capacity]
}

PROCESS Photoinhibition {
 REDUCES: PhotosyntheticPerformance
 UNDER: ExcessExcitationOrDamage
}

PROCESS Photoprotection {
 PROTECTS: PhotosyntheticApparatus
 MAY_INCLUDE: NonPhotochemicalQuenching
}

ENTITY NonPhotochemicalQuenching {
 ABBREVIATION: NPQ
 DISSIPATES: ExcessExcitationEnergy
 AS: Heat
}

ENTITY Stoma {
 IS_A: GasExchangePore
 REGULATES: [CarbonDioxideEntry, WaterVapourLoss]
}

PROCESS PhotosyntheticCarbonAssimilation {
 PRODUCES: ReducedCarbon
 MAY_SUPPORT: [SucroseSynthesis, StarchSynthesis, BiomassProduction]
}

PROCESS PhotosyntheticRegulation {
 MAY_MODULATE: [LightHarvesting, ElectronTransport, ATPFormation, NADPHFormation, CarbonFixation]
}

PROCESS PhotosynthesisMeasurement {
 MAY_MEASURE: [CarbonDioxideAssimilation, OxygenEvolution, ChlorophyllFluorescence, ElectronTransportRate, PigmentAbsorption]
}

ENTITY Evidence {
 TYPES: [BiochemicalEvidence, SpectroscopicEvidence, GasExchangeEvidence, FluorescenceEvidence, IsotopeTracingEvidence, StructuralEvidence, GeneticEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_photosynthetic_models
  RECORD organism
  RECORD tissue_or_cell_type
  RECORD light_conditions
  RECORD carbon_dioxide
  RECORD temperature
  RECORD water_status
  RECORD measurement_method
  RECORD provenance
  REDUCE confidence
 }
}

RELATION Photosynthesis CONVERTS LightEnergy TO ChemicalEnergy
RELATION Chlorophyll ABSORBS LightEnergy
RELATION PhotosystemII OXIDIZES Water
RELATION PhotosyntheticElectronTransport MAY_GENERATE ProtonMotiveForce
RELATION ProtonMotiveForce MAY_DRIVE ATP_Synthase
RELATION PhotosystemI CONTRIBUTES_TO NADPHFormation
RELATION CalvinBensonCycle FIXES CarbonDioxide
RELATION RuBisCO CATALYSES CarbonFixation

SEMANTIC_EQUIVALENCE {
 "photosynthesis" ~= "light-driven biological energy conversion and carbon assimilation" WHEN biological_context
 "PSII" ~= "photosystem II"
 "PSI" ~= "photosystem I"
 "Calvin cycle" ~= "Calvin-Benson cycle"
 "RuBisCO" ~= "ribulose-1,5-bisphosphate carboxylase/oxygenase"
 "NPQ" ~= "non-photochemical quenching"
}

CONFIDENCE PhotosynthesisAssertion {
 INPUTS: [biochemical_support, spectroscopic_support, gas_exchange_support, fluorescence_support, isotope_tracing_support, structural_support, experimental_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 OxygenicPhotosynthesisInference {
 IF water_oxidation
 AND oxygen_evolution
 AND photosystem_activity ARE_SUPPORTED
 THEN OxygenicPhotosynthesis MAY_BE_INFERRED
}

RULE CarbonFixationInference {
 IF labelled_inorganic_carbon enters_organic_metabolites
 THEN CarbonFixation MAY_BE_SUPPORTED
}

RULE C4Inference {
 IF initial_PEP_carboxylation
 AND spatial_carbon_concentration_around_RuBisCO ARE_SUPPORTED
 THEN C4Photosynthesis MAY_BE_INFERRED
}

RULE CAMInference {
 IF temporal_separation_of_initial_carbon_fixation_and_Calvin_cycle IS_SUPPORTED
 THEN CAMPhotosynthesis MAY_BE_INFERRED
}

RULE CausalityConstraint {
 IF chlorophyll_fluorescence correlates_with carbon_assimilation
 THEN DO_NOT_INFER direct_carbon_fixation_rate
 WITHOUT appropriate_calibration_or_gas_exchange_evidence
}

QUERY PhotosynthesisLookup(context_identifier) {
 RETURN [organism, photosynthetic_type, pigments, photosystems, electron_transport, proton_motive_force, ATP_generation, NADPH_generation, carbon_fixation, photorespiration, environmental_conditions, regulation, evidence, confidence]
}

QUERY PhotosystemLookup(photosystem_identifier) {
 RETURN [identity, pigments, reaction_center, electron_donors, electron_acceptors, cofactors, location, photochemical_role, evidence, confidence]
}

QUERY CarbonFixationLookup(context_identifier) {
 RETURN [pathway, carbon_acceptor, fixation_enzyme, ATP_requirement, reducing_power_requirement, intermediates, C3_C4_or_CAM_context, photorespiration, evidence, confidence]
}

UPDATE_MODEL {
 ON new_photosynthesis_evidence:
  validate_provenance()
  identify_organism_tissue_and_cellular_context()
  classify_oxygenic_or_anoxygenic_photosynthesis()
  normalize_pigment_photosystem_and_enzyme_identifiers()
  capture_light_intensity_and_spectrum()
  capture_carbon_dioxide_temperature_and_water_status()
  map_electron_transport_and_photophosphorylation()
  map_carbon_fixation_and_photorespiration()
  classify_C3_C4_or_CAM_context_when_supported()
  capture_measurement_method_and_timepoint()
  compare_existing_photosynthetic_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_photosynthetic_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [photosynthetic_type, organism, pigments, photosystems, electron_transport, ATP_and_NADPH_generation, carbon_fixation, environmental_context, measurement_method, evidence_provenance, confidence]
 REQUIREMENTS: [distinguish_oxygenic_from_anoxygenic_photosynthesis, distinguish_linear_from_cyclic_electron_flow, preserve_species_and_tissue_context, preserve_light_conditions, preserve_carbon_dioxide_temperature_and_water_context, distinguish_light_reactions_from_carbon_fixation, distinguish_C3_C4_and_CAM_strategies, distinguish_fluorescence_from_direct_carbon_flux, distinguish_observation_from_causal_mechanism, preserve_uncertainty]
}

VALIDATE {
 REQUIRE Photosynthesis
 REQUIRE OxygenicPhotosynthesis
 REQUIRE AnoxygenicPhotosynthesis
 REQUIRE PhotosystemII
 REQUIRE PhotosystemI
 REQUIRE PhotosyntheticElectronTransport
 REQUIRE Photophosphorylation
 REQUIRE CalvinBensonCycle
 REQUIRE RuBisCO
 REQUIRE Photorespiration
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT OxygenicPhotosynthesis != AnoxygenicPhotosynthesis
 ASSERT LinearElectronFlow != CyclicElectronFlow
 ASSERT AbsorptionSpectrum != ActionSpectrum
 ASSERT fluorescence != direct_carbon_fixation_rate
 ASSERT correlation != causal_mechanism
}

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 "PhotosynthesisOntology"