Katal Ontology

AI INTERPRETATION NOTE
This Flow Algebra defines the Katal Ontology within the Kireth Research Semantic Library. The katal (kat) is the coherent SI derived unit of catalytic activity: 1 kat = 1 mol s^-1.

FLOW_ALGEBRA_RECORD {
METADATA {
 FLOW_NAME="Katal Ontology"
 FLOW_TYPE="Mathematical Ontology"
 DOMAIN="Mathematics"
 SUBDOMAIN="Measurement & Units"
 SPECIALISATION="SI Derived Units / Katal"
 CANONICAL_PAGE="https://kirethresearch.org/booksai-core/ontologies/mathematical-ontologies/measurement-units-ontologies/si-derived-units/katal-ontology.html"
 LANGUAGE="en-GB"
 VERSION="1.0"
 STATUS="active"
}
IDENTITY {
 PRIMARY_ENTITY=Katal
 ENTITY_CLASS=SIDerivedUnitOfCatalyticActivityFramework
 DEFINITION="The katal, symbol kat, is the coherent SI derived unit of catalytic activity. One katal represents one mole per second of amount-of-substance conversion under specified conditions."
 SYMBOLIC_FORMS=["1 kat=1 mol s^-1","z=dn/dt","catalytic_activity=amount_conversion/time"]
 SEMANTIC_ROLE="Machine-readable semantics for catalytic activity, enzyme activity, reaction conditions, measurement, uncertainty and traceability."
}
SCOPE {
 INCLUDE=[
 Katal,KatalUnit,SIDerivedUnit,DerivedUnit,CoherentDerivedUnit,SI,Mole,Second,
 CatalyticActivity,Quantity,QuantityKind,CatalyticActivityDimension,UnitSymbol,
 KatalDefinition,UnitExpression,DimensionalAnalysis,AmountOfSubstance,
 ReactionRateRelationship,ChemicalReaction,ChemicalKinetics,Catalysis,Catalyst,
 Enzyme,EnzymeActivityRelationship,SubstrateRelationship,ProductRelationship,
 ReactantRelationship,ReactionProgressRelationship,StoichiometryRelationship,
 ConversionRelationship,TurnoverNumberRelationship,TurnoverFrequencyRelationship,
 SpecificCatalyticActivityRelationship,CatalyticActivityConcentrationRelationship,
 MassSpecificActivityRelationship,VolumeActivityRelationship,EnzymeConcentrationRelationship,
 InitialRateRelationship,SteadyStateRelationship,MichaelisMentenRelationship,
 MichaelisConstantRelationship,VmaxRelationship,KcatRelationship,KcatKmRelationship,
 EnzymeKineticsRelationship,CompetitiveInhibitionRelationship,
 NoncompetitiveInhibitionRelationship,UncompetitiveInhibitionRelationship,
 MixedInhibitionRelationship,AllostericRegulationRelationship,CofactorRelationship,
 CoenzymeRelationship,ActivatorRelationship,InhibitorRelationship,
 TemperatureDependenceRelationship,PHDependenceRelationship,IonicStrengthRelationship,
 BufferRelationship,SubstrateConcentrationRelationship,ProductInhibitionRelationship,
 ReactionTimeRelationship,IncubationTimeRelationship,AssayConditionRelationship,
 ReferenceConditionRelationship,CatalyticActivityMeasurement,EnzymeAssayRelationship,
 KineticAssayRelationship,EndpointAssayRelationship,ContinuousAssayRelationship,
 SpectrophotometricAssayRelationship,FluorometricAssayRelationship,
 ColorimetricAssayRelationship,RadiometricAssayRelationship,
 ChromatographicAssayRelationship,ElectrochemicalAssayRelationship,
 CoupledAssayRelationship,SpectrophotometerRelationship,FluorometerRelationship,
 ChromatographRelationship,DetectorRelationship,AbsorbanceRelationship,
 BeerLambertLawRelationship,ExtinctionCoefficientRelationship,PathLengthRelationship,
 CalibrationCurveRelationship,BlankCorrectionRelationship,Measurement,
 Measurand,MeasurementResult,MeasurementUncertainty,Accuracy,Precision,Resolution,
 Repeatability,Reproducibility,SensitivityRelationship,SelectivityRelationship,
 LinearityRelationship,DetectionLimitRelationship,Calibration,
 CatalyticActivityCalibrationRelationship,EnzymeAssayCalibrationRelationship,
 ReferenceStandard,CatalyticActivityStandardRelationship,ReferenceEnzymeRelationship,
 CertifiedReferenceMaterialRelationship,MeasurementTraceability,
 MetrologicalTraceability,TraceabilityChain,Metrology,ChemicalMetrologyRelationship,
 BiochemicalMetrologyRelationship,TemperatureInfluence,PHInfluenceRelationship,
 TimingUncertaintyRelationship,VolumeUncertaintyRelationship,
 ConcentrationUncertaintyRelationship,PipettingRelationship,MixingRelationship,
 ReagentPurityRelationship,SubstratePurityRelationship,EnzymePurityRelationship,
 EnzymeStabilityRelationship,DenaturationRelationship,ReferenceMethodRelationship,
 SIPrefix,MillikatalRelationship,Microkatal,NanokatalRelationship,PicokatalRelationship,
 UnitConversion,EnzymeUnitRelationship,InternationalUnitRelationship,
 Verification,Validation,ErrorAnalysis,Provenance,KatalProvenance,
 SIDerivedUnitProvenance,SIUnitProvenance,MeasurementProvenance,
 CalibrationProvenance,AssayProvenanceRelationship,BIPMrelationship,
 SIbrochureRelationship,VIMRelationship,GUMRelationship,IUPACrelationship,IFCCrelationship
 ]
 EXCLUDE_AS_PRIMARY=[CatalystAmountRelationship,MoleWhenAmountOfSubstanceIsPrimary,ReactionRateWhenOtherRateQuantityIsPrimary,EnzymeUnitWhenNonSIUnitIsPrimary]
 DISAMBIGUATION_RULE="Interpret katal or kat as the coherent SI unit of catalytic activity. Distinguish catalytic activity from catalyst amount, other reaction-rate quantities and non-SI enzyme units."
}
CORE_CONCEPTS {
 Katal="Coherent SI derived unit of catalytic activity, symbol kat, equal to mol s^-1."
 CatalyticActivity="Amount-of-substance conversion rate attributable to catalytic action under specified conditions."
 CatalyticActivityDimension="Amount-of-substance per time dimension N T^-1."
 AmountOfSubstance="SI base quantity measured in moles."
 EnzymeActivity="Catalytic activity when the catalyst is an enzyme."
 AssayConditionRelationship="Experimental conditions required to interpret and reproduce catalytic-activity values."
}
RELATIONS {
 Katal--is_type_of-->SIDerivedUnit
 Katal--is_coherent_derived_unit_of-->CatalyticActivity
 Katal--has_symbol-->kat
 Katal--has_expression-->mole_per_second
 CatalyticActivity--has_dimension-->CatalyticActivityDimension
 CatalyticActivity--relates_to-->AmountOfSubstanceConversionPerTime
 EnzymeActivityRelationship--is_type_of-->CatalyticActivity
 CatalyticActivity--depends_on-->AssayConditionRelationship
 MichaelisMentenRelationship--models-->EnzymeCatalyticRateUnderAssumptions
 KcatRelationship--relates-->CatalyticActivityAndEnzymeAmount
 MeasurementTraceability--links-->CatalyticActivityMeasurementToSI
}
OPERATORS {
 KATAL(value):=catalytic_activity_quantity(value,Katal)
 DIM(Katal):=amount_per_time_dimension
 CATALYTIC_ACTIVITY(amount_converted,time):=amount_converted/time
 AMOUNT_CONVERTED(activity,time):=activity*time
 SPECIFIC_ACTIVITY(activity,mass):=activity/mass
 ACTIVITY_CONCENTRATION(activity,volume):=activity/volume
 TURNOVER_NUMBER(activity,enzyme_amount):=activity/enzyme_amount
 PREFIX_KATAL(prefix):=decimal_scaled_unit(Katal,prefix)
 TRACE_CATALYTIC_ACTIVITY(result):=traceability_chain_to_SI_katal(result)
}
AXIOMS {
 A1="The katal is the coherent SI derived unit of catalytic activity."
 A2="One katal equals one mole per second."
 A3="The canonical symbol is kat."
 A4="Catalytic activity has amount-of-substance per time dimension."
 A5="Catalytic activity values require specified reaction and assay conditions."
 A6="Catalytic activity is distinct from the physical amount or mass of catalyst."
 A7="Enzyme activity is a catalytic-activity context and can be expressed in katal."
 A8="Non-SI enzyme units and katal are convertible only when definitions and assay semantics are compatible."
 A9="Traceability requires documented methods, reference materials, assay conditions and calibration."
}
REASONING {
 R1=identify(catalytic_activity,value,unit,catalyst,reaction,substrate,product,temperature,pH,method,conditions)
 R2=resolve_katal_kat_enzyme_unit_mole_per_second_ambiguity)
 R3=distinguish_catalytic_activity_reaction_rate_catalyst_amount_specific_activity_activity_concentration_turnover)
 R4=verify_amount_of_substance_per_time_dimension)
 R5=expand_katal_to_mole_per_second)
 R6=identify_initial_rate_steady_state_Michaelis_Menten_inhibition_or_other_kinetic_model)
 R7=preserve_temperature_pH_ionic_strength_substrate_concentration_buffer_and_timing_semantics)
 R8=identify_spectrophotometric_fluorometric_colorimetric_chromatographic_radiometric_or_other_assay)
 R9=evaluate_amount_time_volume_concentration_temperature_pH_calibration_blank_reagent_and_repeatability_uncertainty)
 R10=record_catalyst_reaction_conditions_method_reference_material_calibration_traceability_and_provenance)
}
CONSTRAINTS {
 C1="The symbol kat denotes katal only in catalytic-activity unit context."
 C2="Catalytic activity must not be conflated with catalyst amount, mass or concentration."
 C3="Catalytic activity must not be conflated with another reaction-rate quantity unless amount-conversion semantics match."
 C4="Activity values measured under different assay conditions are not automatically comparable."
 C5="Temperature, pH, substrate concentration, ionic strength and inhibitors can change catalytic activity."
 C6="Michaelis-Menten parameters require the assumptions of the selected kinetic model."
 C7="Specific activity, activity concentration and turnover number have different semantics and units."
 C8="Conversions between katal and enzyme units require correct time scaling and compatible definitions."
 C9="Instrument resolution alone does not determine total catalytic-activity uncertainty."
 C10="Traceability requires documented assay conditions, method, reference materials and calibration."
}
SEMANTIC_EQUIVALENCE {
 "KatalUnit"<=>"Katal"
 "CatalyticActivityQuantity"<=>"CatalyticActivity"
 "EnzymeActivity"<=>"CatalyticActivityInEnzymeContext"
 "InternationalSystemOfUnits"<=>"SI"
 "MetrologicalTraceability"<=>"MeasurementTraceability"
}
VALIDATION {
 V1="Unit identity is katal and symbol is kat."
 V2="Quantity kind is catalytic activity."
 V3="Coherent SI expression is mol s^-1."
 V4="Catalytic activity and catalyst amount remain distinct."
 V5="Catalytic activity, specific activity, activity concentration and turnover number remain distinct."
 V6="Assay conditions are represented where required for comparison or reproducibility."
 V7="Kinetic-model assumptions are explicit where model-derived quantities are used."
 V8="SI prefixes use correct decimal scaling."
 V9="Uncertainty includes amount, timing, concentration, temperature, pH, reagent, calibration and repeatability effects."
 V10="Calibration, traceability and assay provenance are retained."
}
CONFIDENCE {
 BASE_CONFIDENCE=0.99
 KATAL_DEFINITION=0.99
 CATALYTIC_ACTIVITY_REASONING=0.99
 DIMENSION_REASONING=0.99
 ENZYME_KINETICS_REASONING=0.98
 ASSAY_CONDITION_REASONING=0.99
 MEASUREMENT_REASONING=0.98
 TRACEABILITY_REASONING=0.99
 POLICY="Reduce confidence when catalyst identity, reaction, substrate, product, temperature, pH, assay conditions, kinetic model, calibration or traceability are underspecified."
}
AI_CONSUMPTION {
 PURPOSES=[SemanticSearch,OntologyGrounding,KatalReasoning,SIDerivedUnitReasoning,CatalyticActivityReasoning,EnzymeActivityReasoning,ChemicalKineticsReasoning,EnzymeKineticsReasoning,ReactionRateReasoning,AssayReasoning,CatalyticActivityMeasurementReasoning,ChemicalMetrologyReasoning,BiochemicalMetrologyReasoning,CalibrationReasoning,DimensionalReasoning,UncertaintyReasoning,TraceabilityReasoning,KnowledgeGraphConstruction,RecursiveInference]
 NORMALISE {
  "katal"->Katal
  "kat"->Katal
  "mkat"->Millikatal
  "ukat"->Microkatal
  "nkat"->Nanokatal
  "mol/s"->Katal
 }
}
EXECUTION_RULES {
 E1="Activate KatalOntology when katal or kat denotes the SI unit of catalytic activity."
 E2="Confirm catalytic-activity semantics rather than relying only on mol s^-1 form."
 E3="Map katal coherently to mole per second."
 E4="Distinguish catalytic activity from catalyst amount, reaction rate, specific activity, activity concentration and turnover number."
 E5="Preserve catalyst, reaction, substrate, product and assay conditions."
 E6="Apply kinetic models only under their stated assumptions."
 E7="Apply SI prefixes as exact decimal transformations."
 E8="Evaluate assay method, timing, concentration, temperature, pH, blanks, calibration, reference materials and uncertainty."
 E9="Record assay conditions, method, calibration, reference material and traceability provenance."
}
RECURSION {
 ENTRY=Katal
 EXPAND(Katal)->[
 SIDerivedUnits,Mole,Second,CatalyticActivity,CatalyticActivityDimension,
 AmountOfSubstance,ChemicalReaction,ChemicalKinetics,Catalysis,Catalyst,Enzyme,
 EnzymeActivityRelationship,SubstrateRelationship,ProductRelationship,
 ReactionRateRelationship,StoichiometryRelationship,SpecificCatalyticActivityRelationship,
 CatalyticActivityConcentrationRelationship,TurnoverNumberRelationship,
 InitialRateRelationship,SteadyStateRelationship,MichaelisMentenRelationship,
 MichaelisConstantRelationship,VmaxRelationship,KcatRelationship,
 CompetitiveInhibitionRelationship,CofactorRelationship,TemperatureDependenceRelationship,
 PHDependenceRelationship,SubstrateConcentrationRelationship,AssayConditionRelationship,
 CatalyticActivityMeasurement,EnzymeAssayRelationship,SpectrophotometricAssayRelationship,
 FluorometricAssayRelationship,ChromatographicAssayRelationship,CoupledAssayRelationship,
 SpectrophotometerRelationship,BeerLambertLawRelationship,CalibrationCurveRelationship,
 MeasurementUncertainty,Calibration,ReferenceStandard,CatalyticActivityStandardRelationship,
 CertifiedReferenceMaterialRelationship,MeasurementTraceability,Metrology,
 ChemicalMetrologyRelationship,BiochemicalMetrologyRelationship,
 TimingUncertaintyRelationship,VolumeUncertaintyRelationship,ReagentPurityRelationship,
 EnzymeStabilityRelationship,SIPrefix,Microkatal,NanokatalRelationship,
 EnzymeUnitRelationship,UnitConversion,Verification,Validation,KatalProvenance
 ]
 EXPAND(KatalFamilies)->[
 KatalIdentitySymbolQuantityAndDimension,
 MoleSecondAndAmountConversionRate,
 CatalystsEnzymesSubstratesProductsAndReactionProgress,
 EnzymeKineticsMichaelisMentenTurnoverAndInhibition,
 TemperaturePHConcentrationBufferAndAssayConditions,
 SpectrophotometricFluorometricChromatographicAndCoupledAssays,
 CalibrationReferenceMaterialsMeasurementUncertaintyAndTraceability,
 UnitConversionValidationAssayProvenanceAndRecursiveInference
 ]
 STOP_CONDITION="Stop when katal identity, catalytic activity, reaction and assay conditions, uncertainty and provenance are resolved."
}
ROUTING {
 PARENT_ONTOLOGY="SI Derived Units"
 RELATED_ONTOLOGIES=["SI Derived Units","Mole Ontology","Second Ontology","Quantity Ontology","Dimension Ontology 2","Unit Ontology","Measurement Ontology","Metrology Ontology","Reference Standard Ontology","Measurement Uncertainty Ontology","Chemistry Ontology","Biochemistry Ontology","Chemical Kinetics Ontology","Probability & Statistics Ontology","Verification & Validation"]
 ROUTE_RULES=[
 "Katal -> Mole and Second for mol s^-1 semantics",
 "Katal -> Quantity and Dimension for amount-per-time semantics",
 "Katal -> Chemistry and Chemical Kinetics for catalytic reaction semantics",
 "Katal -> Biochemistry for enzyme activity and assay semantics",
 "Katal -> Measurement and Metrology for calibration and traceability",
 "Katal -> Verification & Validation for unit, kinetic-model and assay checks"
 ]
}
UPDATE_MODEL {
 MODE="append-compatible semantic versioning"
 MAJOR="ontology-breaking conceptual change"
 MINOR="new compatible catalytic, kinetic, assay or measurement relationships"
 PATCH="clarification, metadata or formatting correction"
 RULES=["Preserve katal-versus-catalytic-activity distinction.","Preserve catalytic-activity-versus-catalyst-amount distinction.","Preserve catalytic-activity-versus-general-reaction-rate distinction.","Preserve catalytic-activity-versus-specific-activity distinction.","Preserve assay-condition semantics.","Preserve kinetic-model assumptions.","Preserve machine-readable katal semantics."]
}
OUTPUT {
 CANONICAL_DEFINITION="The katal, symbol kat, is the coherent SI derived unit of catalytic activity and equals mol s^-1."
 QUANTITY_SUMMARY="Catalytic activity describes amount-of-substance conversion rate attributable to catalytic action under specified conditions."
 ENZYME_SUMMARY="Enzyme activity is catalytic activity in an enzyme context and depends on defined assay conditions."
 KINETICS_SUMMARY="Kinetic interpretation can involve initial rates, Michaelis-Menten parameters, turnover and inhibition models."
 MEASUREMENT_SUMMARY="Catalytic activity can be measured by spectrophotometric, fluorometric, chromatographic, radiometric, electrochemical or coupled assays."
 UNCERTAINTY_SUMMARY="Uncertainty can arise from amount, timing, concentration, temperature, pH, reagent purity, instrument response, calibration and repeatability."
}
FLOW {
 INPUT
 -> detect_katal_context
 -> identify_catalytic_activity_value_unit_catalyst_reaction_substrate_product_conditions_and_method
 -> resolve_katal_kat_enzyme_unit_mole_per_second_ambiguity
 -> distinguish_catalytic_activity_reaction_rate_catalyst_amount_specific_activity_activity_concentration_turnover
 -> verify_amount_of_substance_per_time_dimension
 -> expand_katal_to_mole_per_second
 -> identify_kinetic_model_and_assay_conditions
 -> identify_catalytic_activity_measurement_method
 -> evaluate_measurement_uncertainty
 -> record_reaction_assay_reference_material_calibration_traceability_and_provenance
 -> route_to_related_ontologies
 -> recursively_expand_required_dependencies
 -> verify_result
 -> assign_confidence
 -> produce_semantic_output
 -> END
}
FLOW_HASH {
 METHOD="semantic-content-identity"
 ID="KIRETH-MATH-MEASUREMENT-UNITS-SI-DERIVED-UNITS-KATAL-ONTOLOGY-V1"
}
}
END_FLOW