Biochemistry Ontology

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

flow "BiochemistryCoreOntology" v1.0

ENTITY BiochemistryCoreOntology {
  TYPE: BiologicalOntology
  DOMAIN: Biochemistry
  SUBJECT: BiochemicalSystems
  PURPOSE: FormalSemanticRepresentation
}

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

ENTITY BiochemicalSystem {
  CONTAINS: [Biomolecule, Metabolite, Ion, Water]
  SUPPORTS: BiochemicalProcess
}

ENTITY Biomolecule {
  MAY_BE: [Protein, NucleicAcid, Carbohydrate, Lipid]
}

ENTITY Metabolite {
  IS_A: SmallBiologicalMolecule
  PARTICIPATES_IN: MetabolicReaction
}

ENTITY Protein {
  SUBCLASS_OF: Biomolecule
  COMPOSED_OF: AminoAcid
  HAS: [Sequence, Structure, MolecularFunction]
}

ENTITY Enzyme {
  IS_A: BiologicalCatalyst
  CATALYSES: BiochemicalReaction
  HAS: ActiveSite
  MAY_REQUIRE: Cofactor
}

ENTITY Substrate {
  BINDS_TO: Enzyme
  CONVERTED_TO: Product
}

ENTITY Product {
  PRODUCED_BY: BiochemicalReaction
}

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

RULE EnzymeConservation {
  IF Enzyme CATALYSES Reaction
  THEN Enzyme IS_NOT consumed_stoichiometrically
}

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

ENTITY Coenzyme {
  SUBCLASS_OF: OrganicCofactor
  PARTICIPATES_IN: EnzymeCatalysis
}

ENTITY EnzymeKinetics {
  STUDIES: EnzymeCatalysedReactionRates
  DEPENDS_ON: [SubstrateConcentration, EnzymeConcentration, Temperature, pH, Regulation]
}

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

ENTITY GibbsFreeEnergy { SYMBOL: DeltaG }
ENTITY Enthalpy { SYMBOL: DeltaH }
ENTITY Entropy { SYMBOL: DeltaS }

RULE GibbsEquation {
  DeltaG := DeltaH - Temperature * DeltaS
}

RULE ThermodynamicDirectionRule {
  IF DeltaG < 0
  THEN forward_process IS_THERMODYNAMICALLY_FAVOURABLE
  UNDER specified_conditions
}

RULE KineticThermodynamicDistinction {
  thermodynamic_favourability != reaction_rate
}

ENTITY ChemicalEquilibrium {
  OCCURS_WHEN: ForwardAndReverseRatesAreBalanced
}

ENTITY EquilibriumConstant {
  SYMBOL: Keq
  DESCRIBES: EquilibriumCompositionRelationship
}

ENTITY ATP {
  IS_A: NucleotideTriphosphate
  FUNCTIONS_AS: CellularEnergyCarrier
}

PROCESS EnergyCoupling {
  COUPLES: ExergonicProcess
  TO: EndergonicProcess
}

PROCESS Oxidation { INVOLVES: ElectronLoss }
PROCESS Reduction { INVOLVES: ElectronGain }

ENTITY RedoxReaction {
  COUPLES: [Oxidation, Reduction]
}

ENTITY NADPlus {
  ACCEPTS: Electrons
  MAY_BE_REDUCED_TO: NADH
}

ENTITY NADH {
  MAY_DONATE: Electrons
}

ENTITY pH {
  DESCRIBES: HydrogenIonActivity
  AFFECTS: BiomolecularState
}

ENTITY Buffer {
  RESISTS: pHChange
  WITHIN: EffectiveBufferRange
}

ENTITY NucleicAcid {
  SUBCLASS_OF: Biomolecule
  COMPOSED_OF: Nucleotide
  MAY_BE: [DNA, RNA]
}

ENTITY DNA { STORES: GeneticInformation }
ENTITY RNA { MAY_FUNCTION_IN: [InformationTransfer, Regulation, Catalysis, Translation] }

ENTITY Carbohydrate {
  SUBCLASS_OF: Biomolecule
  MAY_BE: [Monosaccharide, Disaccharide, Oligosaccharide, Polysaccharide]
}

ENTITY Lipid {
  SUBCLASS_OF: Biomolecule
  MAY_INCLUDE: [FattyAcid, Triacylglycerol, Phospholipid, Sterol]
}

ENTITY BiologicalMembrane {
  COMPOSED_OF: [Lipid, Protein]
  SEPARATES: BiologicalCompartments
  CONTROLS: MolecularTransport
}

PROCESS PassiveTransport {
  MOVES: Solute
  DOWN: RelevantGradient
}

PROCESS ActiveTransport {
  MOVES: Solute
  MAY_OPERATE_AGAINST: ElectrochemicalGradient
  REQUIRES: EnergyInput
}

ENTITY Metabolism {
  COMPOSED_OF: MetabolicPathways
  INCLUDES: [Catabolism, Anabolism]
}

PROCESS Catabolism {
  DEGRADES: Molecules
  MAY_GENERATE: EnergyCarriers
}

PROCESS Anabolism {
  SYNTHESIZES: Molecules
  REQUIRES: PrecursorsAndEnergy
}

ENTITY MetabolicPathway {
  COMPOSED_OF: OrderedBiochemicalReactions
  MAY_BE: [Linear, Branched, Cyclic]
}

ENTITY MetabolicIntermediate {
  IS_PRODUCT_OF: UpstreamReaction
  IS_SUBSTRATE_OF: DownstreamReaction
}

ENTITY MetabolicFlux {
  DESCRIBES: RateOfMaterialFlowThroughPathway
}

PROCESS Glycolysis {
  CONVERTS: Glucose
  TO: Pyruvate
  PRODUCES: [ATP, NADH]
}

PROCESS CitricAcidCycle {
  OXIDIZES: AcetylCoA
  GENERATES: ReducedElectronCarriers
}

PROCESS OxidativePhosphorylation {
  COUPLES: ElectronTransport
  TO: ATPProduction
}

PROCESS MolecularBinding {
  INPUTS: [MoleculeA, MoleculeB]
  OUTPUT: MolecularComplex
}

ENTITY BindingAffinity {
  DESCRIBES: StrengthOfMolecularAssociation
}

ENTITY DissociationConstant { SYMBOL: Kd }

ENTITY Receptor {
  BINDS: Ligand
  MAY_INITIATE: SignalTransduction
}

PROCESS SignalTransduction {
  TRANSMITS: MolecularSignal
  MAY_MODIFY: CellularState
}

PROCESS BiochemicalRegulation {
  MAY_MODULATE: [EnzymeActivity, MetabolicFlux, Transport, Signalling]
}

PROCESS FeedbackInhibition {
  OCCURS_WHEN: DownstreamProductInhibitsUpstreamProcess
}

PROCESS PostTranslationalModification {
  TARGET: Protein
  MAY_INCLUDE: [Phosphorylation, Glycosylation, Acetylation, Ubiquitination]
  MAY_CHANGE: [Activity, Stability, Localization, Interactions]
}

ENTITY BiochemicalHomeostasis {
  MAINTAINS: MolecularVariables
  WITHIN: FunctionalRange
}

ENTITY ExperimentalContext {
  MAY_INCLUDE: [organism, cell_type, compartment, temperature, pH, ionic_strength, concentration, assay_method, timepoint]
}

PROCESS BiochemicalMeasurement {
  MAY_MEASURE: [Concentration, ReactionRate, BindingAffinity, EnzymeActivity, MetaboliteAbundance]
}

RULE ContextPreservation {
  IF biochemical_results ARE_COMPARED
  THEN ExperimentalContext MUST_BE preserved
}

ENTITY Evidence {
  TYPES: [BiochemicalEvidence, KineticEvidence, StructuralEvidence, MetabolomicEvidence, ProteomicEvidence, MolecularEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

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

RULE EvidenceConflict {
  IF EvidenceSources CONFLICT
  THEN {
    PRESERVE competing_assertions
    RECORD molecular_identity
    RECORD reaction_conditions
    RECORD assay_method
    RECORD cellular_context
    RECORD provenance
    REDUCE confidence
    REQUIRE further_validation
  }
}

RELATION Biomolecule PART_OF BiochemicalSystem
RELATION Enzyme CATALYSES BiochemicalReaction
RELATION Substrate CONVERTED_TO Product
RELATION Cofactor ASSISTS Enzyme
RELATION Metabolite PARTICIPATES_IN MetabolicPathway
RELATION ATP PARTICIPATES_IN EnergyCoupling
RELATION MolecularBinding FORMS MolecularComplex
RELATION MetabolicPathway PART_OF Metabolism

SEMANTIC_EQUIVALENCE {
  "biochemical system" ~= "biological chemical system"
  "biochemical reaction" ~= "reaction in biological context"
  "metabolic intermediate" ~= "pathway intermediate"
  "enzyme activity" ~= "catalytic activity" WHEN enzyme_context_is_defined
  "binding affinity" ~= "molecular affinity" WHEN binding_context_is_defined
}

RULE EquivalenceConstraint {
  IF terms ARE semantic_equivalents
  THEN preserve_molecular_identity()
  AND preserve_reaction_identity()
  AND preserve_cellular_context()
  AND preserve_experimental_conditions()
  AND prevent_false_identity()
}

CONFIDENCE BiochemistryAssertion {
  INPUTS: [experimental_support, biochemical_support, kinetic_support, structural_support, analytical_quality, biological_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"
}

RULE ReactionInference {
  IF Enzyme catalyses Reaction
     AND Reaction converts Substrate TO Product
  THEN catalytic_relationship := supported
}

RULE PathwayInference {
  IF ReactionA produces Intermediate
     AND ReactionB consumes Intermediate
  THEN pathway_connection MAY_BE_SUPPORTED
}

RULE ThermodynamicInference {
  IF DeltaG < 0 under_defined_conditions
  THEN process IS_THERMODYNAMICALLY_FAVOURABLE
  BUT rate := unresolved_without_kinetics
}

RULE CausalityConstraint {
  IF biochemical_association IS_OBSERVED
  THEN DO_NOT_INFER causal_cellular_effect
  WITHOUT functional_evidence
}

QUERY BiochemicalEntityLookup(identifier) {
  RETURN [identity, molecular_class, structure, function, reactions, interactions, pathways, cellular_context, measurements, evidence, confidence]
}

QUERY ReactionLookup(reaction_identifier) {
  RETURN [reactants, products, stoichiometry, enzymes, cofactors, DeltaG, kinetics, regulation, pathway_context, evidence, confidence]
}

QUERY PathwayLookup(pathway_identifier) {
  RETURN [inputs, reactions, enzymes, cofactors, intermediates, outputs, energy_transfer, flux, regulation, cellular_context, evidence, confidence]
}

UPDATE_MODEL {
  ON new_biochemistry_evidence:
    validate_provenance()
    identify_organism_and_cellular_context()
    normalize_molecular_identifiers()
    normalize_reaction_identifiers()
    validate_stoichiometry()
    capture_temperature_pH_and_assay_conditions()
    map_enzymes_substrates_products_and_cofactors()
    compare_existing_assertions()
    preserve_conflicting_evidence()
    recalculate_confidence()
    regenerate_pathway_and_interaction_links()
    update_flow_hash()
}

AI_CONSUMPTION {
  MODE: FormalSemanticReasoning
  PARSE_AS: ExecutableFlowAlgebra
  PRIORITIES: [molecular_identity, reaction_identity, stoichiometry, enzyme_context, thermodynamics, kinetics, pathway_context, cellular_context, evidence_provenance, confidence]
  REQUIREMENTS: [
    distinguish_substrate_from_product,
    distinguish_enzyme_from_reaction,
    preserve_molecular_identity,
    preserve_cellular_context,
    preserve_temperature_and_pH,
    preserve_assay_conditions,
    distinguish_thermodynamic_favourability_from_reaction_rate,
    distinguish_binding_from_catalysis,
    distinguish_observed_from_inferred_function,
    avoid_unsupported_causal_inference
  ]
}

VALIDATE {
  REQUIRE BiochemicalSystem
  REQUIRE Biomolecule
  REQUIRE Enzyme
  REQUIRE EnzymeCatalysis
  REQUIRE Metabolism
  REQUIRE MetabolicPathway
  REQUIRE GibbsFreeEnergy
  REQUIRE ATP
  REQUIRE MolecularBinding
  REQUIRE Evidence
  REQUIRE CONFIDENCE
  REQUIRE SEMANTIC_EQUIVALENCE
  REQUIRE UPDATE_MODEL
  REQUIRE AI_CONSUMPTION

  ASSERT Enzyme != BiochemicalReaction
  ASSERT thermodynamic_favourability != reaction_rate
  ASSERT binding != catalysis
  ASSERT biochemical_association != causal_function
}

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 "BiochemistryCoreOntology"