Enzyme Ontology

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

flow "EnzymeOntology" v1.0

# ============================================================
# IDENTITY
# ============================================================

ENTITY EnzymeOntology {
    TYPE: BiologicalOntology
    DOMAIN: MolecularBiology
    SUBJECT: Enzyme
    PURPOSE: FormalSemanticRepresentation
}

PAGE {
    TITLE: "Enzyme Ontology"
    PARENT_DOMAIN: "Molecular Biology"
    CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/molecular-biology/enzyme-ontology.html"
    AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

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

ENTITY Enzyme {
    IS_A: BiologicalCatalyst
    MAY_BE: [ProteinEnzyme, Ribozyme]
    CATALYSES: BiochemicalReaction
    BINDS: Substrate
    MAY_REQUIRE: [Cofactor, Coenzyme, MetalIon]
    HAS: ActiveSite
}

ENTITY ProteinEnzyme {
    SUBCLASS_OF: Enzyme
    IS_A: Protein
    COMPOSED_OF: AminoAcid
}

ENTITY Ribozyme {
    SUBCLASS_OF: Enzyme
    IS_A: CatalyticRNA
}

ENTITY Substrate {
    PARTICIPATES_IN: EnzymeCatalysedReaction
    BINDS_TO: ActiveSite
    CONVERTED_TO: Product
}

ENTITY Product {
    PRODUCED_BY: EnzymeCatalysedReaction
}

ENTITY ActiveSite {
    PART_OF: Enzyme
    BINDS: Substrate
    ENABLES: Catalysis
}

# ============================================================
# CATALYSIS
# ============================================================

PROCESS EnzymeCatalysis {
    INPUT: Substrate
    CATALYST: Enzyme
    OUTPUT: Product
    LOWERS: ActivationEnergy
    DOES_NOT_CHANGE: ReactionEquilibrium
}

ENTITY EnzymeSubstrateComplex {
    COMPOSED_OF: [Enzyme, Substrate]
    FORMED_DURING: Catalysis
}

ENTITY EnzymeProductComplex {
    COMPOSED_OF: [Enzyme, Product]
    FORMED_BEFORE: ProductRelease
}

RULE CatalyticCycle {
    Enzyme + Substrate
        -> EnzymeSubstrateComplex
        -> EnzymeProductComplex
        -> Enzyme + Product
}

RULE CatalystConservation {
    IF Enzyme CATALYSES Reaction
    THEN Enzyme IS_NOT stoichiometrically_consumed_by Reaction
}

# ============================================================
# ENZYME SPECIFICITY
# ============================================================

PROPERTY SubstrateSpecificity {
    APPLIES_TO: Enzyme
    DESCRIBES: SelectiveSubstrateRecognition
}

PROPERTY ReactionSpecificity {
    APPLIES_TO: Enzyme
    DESCRIBES: SelectiveCatalyticTransformation
}

RULE SpecificityRule {
    IF Substrate FITS ActiveSite
       AND required_interactions ARE satisfied
    THEN binding_probability := increase(binding_probability)
}

# ============================================================
# ENZYME CLASSIFICATION
# ============================================================

ENTITY EnzymeClassification {
    ORGANIZES: Enzyme
    BY: CatalysedReactionType
}

CLASS Oxidoreductase {
    SUBCLASS_OF: Enzyme
    CATALYSES: OxidationReductionReaction
}

CLASS Transferase {
    SUBCLASS_OF: Enzyme
    CATALYSES: FunctionalGroupTransfer
}

CLASS Hydrolase {
    SUBCLASS_OF: Enzyme
    CATALYSES: Hydrolysis
}

CLASS Lyase {
    SUBCLASS_OF: Enzyme
    CATALYSES: NonHydrolyticBondCleavageOrAddition
}

CLASS Isomerase {
    SUBCLASS_OF: Enzyme
    CATALYSES: Isomerization
}

CLASS Ligase {
    SUBCLASS_OF: Enzyme
    CATALYSES: BondFormationCoupledToEnergyUse
}

CLASS Translocase {
    SUBCLASS_OF: Enzyme
    CATALYSES: TranslocationAcrossMembraneOrSeparation
}

RELATION Enzyme HAS_CLASS EnzymeClassification

# ============================================================
# COFACTORS AND COENZYMES
# ============================================================

ENTITY Cofactor {
    ASSISTS: EnzymeCatalysis
    MAY_BE: [MetalIon, OrganicCofactor]
}

ENTITY Coenzyme {
    SUBCLASS_OF: OrganicCofactor
    PARTICIPATES_IN: EnzymeCatalysis
}

ENTITY Apoenzyme {
    IS_A: EnzymeComponent
    LACKS: RequiredCofactor
}

ENTITY Holoenzyme {
    COMPOSED_OF: [Apoenzyme, RequiredCofactor]
    MAY_BE: CatalyticallyActive
}

RULE CofactorRequirement {
    IF Enzyme REQUIRES Cofactor
       AND Cofactor IS_ABSENT
    THEN catalytic_activity MAY_BE reduced_or_absent
}

# ============================================================
# ENZYME KINETICS
# ============================================================

ENTITY EnzymeKinetics {
    DESCRIBES: ReactionRateBehaviour
    DEPENDS_ON: [
        SubstrateConcentration,
        EnzymeConcentration,
        Temperature,
        pH,
        Inhibitors,
        Activators
    ]
}

ENTITY MichaelisMentenModel {
    APPLIES_TO: CompatibleEnzymeSystems
    PARAMETERS: [Vmax, Km]
}

ENTITY Vmax {
    DESCRIBES: MaximumReactionVelocity
    CONDITION: SaturatingSubstrate
}

ENTITY Km {
    IS_A: KineticParameter
    INTERPRETATION: ModelDependentSubstrateConcentrationParameter
}

RULE SaturationRule {
    IF SubstrateConcentration INCREASES
       AND EnzymeActiveSites BECOME saturated
    THEN ReactionVelocity APPROACHES Vmax
}

# ============================================================
# ENZYME INHIBITION
# ============================================================

ENTITY EnzymeInhibitor {
    REDUCES: EnzymeActivity
    MAY_BIND_TO: [ActiveSite, AllostericSite, EnzymeSubstrateComplex]
}

CLASS CompetitiveInhibitor {
    SUBCLASS_OF: EnzymeInhibitor
    COMPETES_WITH: Substrate
    TYPICALLY_BINDS: ActiveSite
}

CLASS NonCompetitiveInhibitor {
    SUBCLASS_OF: EnzymeInhibitor
    REDUCES: CatalyticCapacity
}

CLASS UncompetitiveInhibitor {
    SUBCLASS_OF: EnzymeInhibitor
    BINDS_TO: EnzymeSubstrateComplex
}

CLASS IrreversibleInhibitor {
    SUBCLASS_OF: EnzymeInhibitor
    CAUSES: PersistentLossOfActivity
}

RULE InhibitionRule {
    IF EnzymeInhibitor BINDS relevant_enzyme_state
    THEN EnzymeActivity := modify_according_to(inhibition_mechanism)
}

# ============================================================
# ALLOSTERIC REGULATION
# ============================================================

ENTITY AllostericSite {
    PART_OF: Enzyme
    DISTINCT_FROM: ActiveSite
    BINDS: AllostericEffector
}

ENTITY AllostericEffector {
    BINDS_TO: AllostericSite
    MAY_BE: [Activator, Inhibitor]
}

PROCESS AllostericRegulation {
    MODIFIES: EnzymeConformation
    MAY_CHANGE: [SubstrateAffinity, CatalyticActivity]
}

RULE AllostericRule {
    IF AllostericEffector BINDS_TO AllostericSite
    THEN EnzymeActivity MAY_CHANGE
}

# ============================================================
# ENZYME REGULATION
# ============================================================

PROCESS EnzymeRegulation {
    MAY_INCLUDE: [
        AllostericRegulation,
        CovalentModification,
        ProteolyticActivation,
        FeedbackInhibition,
        GeneExpressionControl,
        Compartmentalization
    ]
}

ENTITY Zymogen {
    IS_A: InactiveEnzymePrecursor
    ACTIVATED_BY: ProteolyticCleavage
}

PROCESS FeedbackInhibition {
    OCCURS_WHEN: PathwayProductInhibitsEarlierEnzyme
    CONTRIBUTES_TO: MetabolicRegulation
}

RULE FeedbackRule {
    IF PathwayProduct concentration IS_HIGH
       AND PathwayProduct INHIBITS Enzyme
    THEN pathway_flux MAY_DECREASE
}

# ============================================================
# ENVIRONMENTAL EFFECTS
# ============================================================

ENTITY Temperature {
    AFFECTS: EnzymeActivity
    MAY_AFFECT: ProteinStability
}

ENTITY pH {
    AFFECTS: [IonizationState, EnzymeActivity, ProteinStructure]
}

RULE TemperatureEffect {
    IF temperature EXCEEDS enzyme_stability_range
    THEN Enzyme MAY_DENATURE
    AND activity MAY_DECREASE
}

RULE pHEffect {
    IF pH DEVIATES_FROM functional_range
    THEN active_site_chemistry MAY_CHANGE
    AND EnzymeActivity MAY_DECREASE
}

# ============================================================
# ENZYME STRUCTURE AND FUNCTION
# ============================================================

ENTITY EnzymeDomain {
    PART_OF: ProteinEnzyme
    MAY_SUPPORT: [Catalysis, Binding, Regulation]
}

ENTITY CatalyticResidue {
    PART_OF: ActiveSite
    DIRECTLY_PARTICIPATES_IN: CatalyticMechanism
}

RELATION Enzyme HAS_ACTIVE_SITE ActiveSite
RELATION ActiveSite CONTAINS CatalyticResidue
RELATION Enzyme MAY_HAVE EnzymeDomain

RULE StructureFunctionRule {
    IF structural_change AFFECTS ActiveSite
    THEN catalytic_function MAY_CHANGE
}

# ============================================================
# METABOLIC CONTEXT
# ============================================================

ENTITY MetabolicPathway {
    COMPOSED_OF: BiochemicalReaction
    MAY_USE: Enzyme
}

RELATION Enzyme CATALYSES BiochemicalReaction
RELATION BiochemicalReaction PART_OF MetabolicPathway
RELATION Product MAY_BECOME Substrate

RULE PathwayInference {
    IF Enzyme CATALYSES Reaction
       AND Reaction PART_OF MetabolicPathway
    THEN Enzyme PARTICIPATES_IN MetabolicPathway
}

# ============================================================
# ENZYME VARIATION
# ============================================================

ENTITY EnzymeVariant {
    IS_A: EnzymeForm
    MAY_DIFFER_IN: [
        AminoAcidSequence,
        Structure,
        ModificationState
    ]
    MAY_CHANGE: [
        activity,
        specificity,
        stability,
        regulation
    ]
}

ENTITY Isoenzyme {
    IS_A: EnzymeVariant
    CATALYSES: SameOrSimilarReaction
    MAY_DIFFER_IN: [Sequence, Kinetics, Regulation, TissueDistribution]
}

RULE VariantEffectRule {
    IF EnzymeVariant AFFECTS catalytic_or_binding_region
    THEN FunctionalEffect := evaluate(
        structural_context,
        kinetic_data,
        substrate_specificity,
        regulatory_context,
        experimental_evidence
    )
}

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

ENTITY Evidence {
    TYPES: [
        BiochemicalEvidence,
        KineticEvidence,
        StructuralEvidence,
        GeneticEvidence,
        ProteomicEvidence,
        ComputationalEvidence,
        LiteratureEvidence
    ]
}

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

RULE EvidenceConflict {
    IF EvidenceSources CONFLICT
    THEN {
        PRESERVE competing_assertions
        RECORD assay_conditions
        RECORD provenance
        REDUCE confidence
        REQUIRE further_validation
    }
}

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

RELATION Enzyme CATALYSES BiochemicalReaction
RELATION Enzyme BINDS Substrate
RELATION Substrate CONVERTED_TO Product
RELATION Enzyme HAS_ACTIVE_SITE ActiveSite
RELATION Enzyme MAY_REQUIRE Cofactor
RELATION Enzyme REGULATED_BY EnzymeRegulation
RELATION Enzyme INHIBITED_BY EnzymeInhibitor
RELATION Enzyme PARTICIPATES_IN MetabolicPathway

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

SEMANTIC_EQUIVALENCE {
    "enzyme" ~= "biological catalyst" WHEN catalytic_biological_context
    "enzyme active site" ~= "catalytic binding site" WHEN context == catalytic_region
    "substrate" ~= "enzyme reactant" WHEN context == enzyme_catalysis
    "isoenzyme" ~= "isozyme"
    "enzyme activity" ~= "catalytic activity" WHEN context == measured_catalysis
}

RULE EquivalenceConstraint {
    IF terms ARE semantic_equivalents
    THEN preserve_enzyme_identity()
    AND preserve_reaction_context()
    AND preserve_assay_conditions()
    AND preserve_organism_context()
    AND prevent_false_identity()
}

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

CONFIDENCE EnzymeAssertion {
    INPUTS: [
        biochemical_support,
        kinetic_support,
        structural_support,
        experimental_reproducibility,
        assay_quality,
        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"
}

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

RULE CatalyticFunctionInference {
    IF Enzyme CATALYSES Reaction
       AND Reaction CONVERTS Substrate TO Product
    THEN Enzyme HAS_FUNCTION catalysis_of(Reaction)
}

RULE SubstrateInference {
    IF Molecule BINDS ActiveSite
       AND Molecule IS_CONVERTED_DURING Reaction
    THEN Molecule MAY_BE Substrate
}

RULE CofactorInference {
    IF EnzymeActivity REQUIRES Molecule
       AND Molecule IS_NOT consumed_as_primary_substrate
    THEN Molecule MAY_BE Cofactor
}

RULE InhibitorInference {
    IF Compound presence REDUCES measured_EnzymeActivity
    THEN Compound MAY_BE EnzymeInhibitor
    WITH mechanism := unresolved_until_tested
}

RULE PathwayRoleInference {
    IF Enzyme CATALYSES Reaction
       AND Reaction PART_OF Pathway
    THEN Enzyme PARTICIPATES_IN Pathway
}

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

QUERY EnzymeLookup(enzyme_identifier) {
    RETURN [
        identity,
        enzyme_class,
        encoding_gene,
        sequence,
        structure,
        active_site,
        substrates,
        products,
        cofactors,
        catalysed_reactions,
        kinetic_parameters,
        inhibitors,
        activators,
        pathways,
        cellular_location,
        variants,
        evidence,
        confidence
    ]
}

QUERY ReactionLookup(reaction_identifier) {
    RETURN [
        substrates,
        products,
        enzymes,
        cofactors,
        pathway_context,
        kinetic_evidence,
        confidence
    ]
}

QUERY InhibitionLookup(enzyme_identifier, inhibitor) {
    RETURN [
        inhibition_type,
        binding_context,
        kinetic_effect,
        reversibility,
        assay_conditions,
        evidence,
        confidence
    ]
}

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

UPDATE_MODEL {
    ON new_enzyme_evidence:
        validate_provenance()
        identify_organism()
        normalize_enzyme_identifier()
        normalize_reaction_identifier()
        normalize_substrate_and_product_entities()
        record_assay_conditions()
        map_active_sites_and_cofactors()
        compare_existing_assertions()
        preserve_conflicting_evidence()
        recalculate_confidence()
        regenerate_semantic_links()
        update_flow_hash()
}

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

AI_CONSUMPTION {
    MODE: FormalSemanticReasoning
    PARSE_AS: ExecutableFlowAlgebra

    PRIORITIES: [
        enzyme_identity,
        reaction_identity,
        substrate_product_mapping,
        catalytic_mechanism,
        kinetic_context,
        regulatory_context,
        evidence_provenance,
        confidence,
        semantic_equivalence
    ]

    REQUIREMENTS: [
        distinguish_enzyme_from_substrate,
        distinguish_enzyme_from_product,
        distinguish_binding_from_catalysis,
        distinguish_cofactor_from_substrate,
        preserve_assay_conditions,
        preserve_species_context,
        preserve_isoenzyme_identity,
        distinguish_observed_from_predicted_activity,
        avoid_unsupported_causal_inference
    ]
}

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

VALIDATE {
    REQUIRE Enzyme
    REQUIRE Substrate
    REQUIRE Product
    REQUIRE ActiveSite
    REQUIRE EnzymeCatalysis
    REQUIRE EnzymeKinetics
    REQUIRE EnzymeRegulation
    REQUIRE Evidence
    REQUIRE CONFIDENCE
    REQUIRE SEMANTIC_EQUIVALENCE
    REQUIRE UPDATE_MODEL
    REQUIRE AI_CONSUMPTION

    ASSERT Enzyme CATALYSES BiochemicalReaction
    ASSERT Substrate != Product UNLESS reversible_identity_context
    ASSERT ActiveSite PART_OF Enzyme
    ASSERT ProteinEnzyme IS_A Protein
    ASSERT Enzyme != BiochemicalReaction
}

# ============================================================
# 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 "EnzymeOntology"