Carbohydrate Ontology

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

flow "CarbohydrateOntology" v1.0

ENTITY CarbohydrateOntology {
 TYPE: BiologicalOntology
 DOMAIN: Biochemistry
 SUBJECT: Carbohydrate
 PURPOSE: FormalSemanticRepresentation
}

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

ENTITY Carbohydrate {
 IS_A: Biomolecule
 MAY_BE: [Monosaccharide, Disaccharide, Oligosaccharide, Polysaccharide]
 MAY_FUNCTION_IN: [Energy, EnergyStorage, Structure, Recognition, Signalling]
}

ENTITY Monosaccharide {
 IS_A: SimpleCarbohydrate
 MAY_FORM: LargerCarbohydrate
}

ENTITY Aldose { SUBCLASS_OF: Monosaccharide }
ENTITY Ketose { SUBCLASS_OF: Monosaccharide }
ENTITY Pentose { SUBCLASS_OF: Monosaccharide; CARBON_COUNT: 5 }
ENTITY Hexose { SUBCLASS_OF: Monosaccharide; CARBON_COUNT: 6 }

ENTITY Glucose {
 SUBCLASS_OF: Aldohexose
 PARTICIPATES_IN: CentralMetabolism
}

ENTITY Fructose { SUBCLASS_OF: Ketohexose }
ENTITY Galactose { SUBCLASS_OF: Aldohexose }
ENTITY Ribose { SUBCLASS_OF: Aldopentose; PART_OF: RNA_Nucleotides }
ENTITY Deoxyribose { SUBCLASS_OF: Pentose; PART_OF: DNA_Nucleotides }

ENTITY CarbohydrateStereochemistry {
 MAY_INCLUDE: [DConfiguration, LConfiguration, Epimerism, Anomerism]
}

ENTITY Epimer {
 RELATES: Monosaccharides
 DIFFER_AT: OneSpecifiedStereogenicCenter
}

ENTITY Anomer {
 RELATES: CyclicSugarForms
 DIFFER_AT: AnomericCarbonConfiguration
}

PROCESS RingFormation {
 CONVERTS: OpenChainMonosaccharide
 TO: CyclicMonosaccharide
}

ENTITY Pyranose { IS_A: SixMemberedSugarRingForm }
ENTITY Furanose { IS_A: FiveMemberedSugarRingForm }

PROCESS Mutarotation {
 INTERCONVERTS: AlphaAndBetaAnomers
 THROUGH: OpenChainIntermediate
}

ENTITY GlycosidicBond {
 IS_A: CovalentBond
 CONNECTS: SugarResidues
 HAS: [AnomericConfiguration, LinkagePositions]
}

PROCESS GlycosidicBondFormation {
 JOINS: SugarResidues
 MAY_RELEASE: Water
}

PROCESS GlycosidicBondHydrolysis {
 CLEAVES: GlycosidicBond
 USES: Water
}

RULE LinkageIdentityRule {
 CarbohydrateStructure DEPENDS_ON [residue_identity, anomeric_configuration, linkage_positions, branching]
}

ENTITY Disaccharide {
 SUBCLASS_OF: Carbohydrate
 COMPOSED_OF: TwoSugarResidues
}

ENTITY Sucrose {
 SUBCLASS_OF: Disaccharide
 COMPOSED_OF: [GlucoseResidue, FructoseResidue]
}

ENTITY Lactose {
 SUBCLASS_OF: Disaccharide
 COMPOSED_OF: [GalactoseResidue, GlucoseResidue]
}

ENTITY Maltose {
 SUBCLASS_OF: Disaccharide
 COMPOSED_OF: [GlucoseResidue, GlucoseResidue]
}

ENTITY Oligosaccharide {
 SUBCLASS_OF: Carbohydrate
 COMPOSED_OF: SmallNumberOfSugarResidues
 MAY_BE: [Linear, Branched]
}

ENTITY Glycan {
 IS_A: CarbohydrateStructure
 MAY_BE: [Oligosaccharide, Polysaccharide]
}

ENTITY Polysaccharide {
 SUBCLASS_OF: Carbohydrate
 COMPOSED_OF: ManySugarResidues
 MAY_BE: [Homopolysaccharide, Heteropolysaccharide]
}

ENTITY Starch {
 SUBCLASS_OF: StoragePolysaccharide
 COMPOSED_PRIMARILY_OF: GlucoseResidues
}

ENTITY Glycogen {
 SUBCLASS_OF: StoragePolysaccharide
 COMPOSED_PRIMARILY_OF: GlucoseResidues
 HIGHLY_BRANCHED: true
}

ENTITY Cellulose {
 SUBCLASS_OF: StructuralPolysaccharide
 COMPOSED_OF: GlucoseResidues
 HAS: BetaLinkedBackbone
}

ENTITY Chitin {
 SUBCLASS_OF: StructuralPolysaccharide
 COMPOSED_OF: ModifiedSugarResidues
}

ENTITY ReducingSugar {
 IS_A: Carbohydrate
 HAS: ChemicallyAvailableReducingEnd
}

PROCESS CarbohydrateMetabolism {
 INCLUDES: [Glycolysis, Glycogenesis, Glycogenolysis, Gluconeogenesis, PentosePhosphatePathway]
}

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

PROCESS Glycogenesis {
 SYNTHESIZES: Glycogen
 FROM: ActivatedGlucosePrecursors
}

PROCESS Glycogenolysis {
 DEGRADES: Glycogen
 PRODUCES: GlucoseDerivedProducts
}

PROCESS Gluconeogenesis {
 SYNTHESIZES: Glucose
 FROM: NonCarbohydratePrecursors
}

PROCESS PentosePhosphatePathway {
 PRODUCES: [NADPH, PentosePhosphates]
}

PROCESS CarbohydrateDigestion {
 HYDROLYSES: DietaryCarbohydrates
 PRODUCES: AbsorbableSugars
}

ENTITY Glycosidase {
 IS_A: Enzyme
 CATALYSES: GlycosidicBondHydrolysis
}

PROCESS Glycosylation {
 ATTACHES: CarbohydrateMoiety
 TO: Biomolecule
 MAY_TARGET: [Protein, Lipid]
}

ENTITY Glycoprotein {
 COMPOSED_OF: [Protein, CovalentlyAttachedCarbohydrate]
}

ENTITY Glycolipid {
 COMPOSED_OF: [Lipid, CovalentlyAttachedCarbohydrate]
}

ENTITY Lectin {
 IS_A: CarbohydrateBindingProtein
 BINDS: SpecificCarbohydrateStructures
}

ENTITY Glycosaminoglycan {
 ABBREVIATION: GAG
 IS_A: Polysaccharide
 OFTEN_COMPOSED_OF: RepeatingDisaccharideUnits
}

ENTITY Proteoglycan {
 COMPOSED_OF: [CoreProtein, GlycosaminoglycanChains]
 CONTRIBUTES_TO: ExtracellularMatrix
}

PROCESS SugarTransport {
 MOVES: Monosaccharide
 ACROSS: BiologicalMembrane
}

ENTITY SugarTransporter {
 IS_A: MembraneProtein
 TRANSPORTS: Sugar
}

PROCESS CarbohydrateBiosynthesis {
 PRODUCES: Carbohydrate
 MAY_REQUIRE: [ActivatedSugarDonor, Glycosyltransferase]
}

ENTITY Glycosyltransferase {
 IS_A: Enzyme
 TRANSFERS: SugarResidue
 TO: AcceptorMolecule
}

PROCESS CarbohydrateDegradation {
 BREAKS_DOWN: Carbohydrate
 MAY_USE: [Hydrolase, Lyase]
}

PROCESS CarbohydrateAnalysis {
 MAY_DETERMINE: [MonosaccharideComposition, LinkagePattern, Branching, MolecularMass, Stereochemistry, GlycanStructure]
 MAY_USE: [MassSpectrometry, Chromatography, NuclearMagneticResonance, EnzymaticAnalysis]
}

ENTITY Evidence {
 TYPES: [BiochemicalEvidence, StructuralEvidence, MassSpectrometricEvidence, ChromatographicEvidence, NMREvidence, EnzymaticEvidence, MetabolomicEvidence, ComputationalEvidence, LiteratureEvidence]
}

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_structural_assignments
  RECORD carbohydrate_identity
  RECORD stereochemistry
  RECORD linkage_pattern
  RECORD biological_context
  RECORD analytical_method
  RECORD provenance
  REDUCE confidence
 }
}

RELATION Carbohydrate COMPOSED_OF SugarResidue
RELATION SugarResidue CONNECTED_BY GlycosidicBond
RELATION Monosaccharide MAY_FORM Oligosaccharide
RELATION Polysaccharide IS_A Glycan
RELATION Glycosylation ATTACHES Carbohydrate TO Biomolecule
RELATION Lectin BINDS Glycan
RELATION Carbohydrate PARTICIPATES_IN CarbohydrateMetabolism

SEMANTIC_EQUIVALENCE {
 "carbohydrate" ~= "saccharide" WHEN broad_biochemical_context
 "simple sugar" ~= "monosaccharide" WHEN single_sugar_unit_context
 "glycosidic linkage" ~= "glycosidic bond"
 "GAG" ~= "glycosaminoglycan"
}

CONFIDENCE CarbohydrateAssertion {
 INPUTS: [chemical_identity_support, stereochemical_support, linkage_support, structural_support, analytical_quality, biochemical_support, 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 CarbohydrateClassification {
 IF molecular_structure matches_defined_saccharide_features
 THEN classify_by [residue_count, carbon_count, carbonyl_type, stereochemistry, linkage, branching]
}

RULE GlycanInference {
 IF multiple_sugar_residues ARE_CONNECTED_BY glycosidic_bonds
 THEN Glycan MAY_EXIST
}

RULE CausalityConstraint {
 IF carbohydrate_abundance correlates_with biological_state
 THEN DO_NOT_INFER causal_role
 WITHOUT functional_evidence
}

QUERY CarbohydrateLookup(identifier) {
 RETURN [identity, carbohydrate_class, monosaccharide_composition, stereochemistry, ring_form, glycosidic_linkages, branching, molecular_mass, biological_functions, metabolic_pathways, conjugates, evidence, confidence]
}

QUERY GlycanLookup(identifier) {
 RETURN [residues, sequence_or_topology, linkages, branching, attachment_site, parent_biomolecule, recognition_partners, biological_context, evidence, confidence]
}

UPDATE_MODEL {
 ON new_carbohydrate_evidence:
  validate_provenance()
  normalize_carbohydrate_identifier()
  identify_organism_and_biological_context()
  determine_monosaccharide_composition()
  determine_stereochemistry()
  normalize_glycosidic_linkages()
  map_branching_and_topology()
  map_metabolic_and_glycosylation_relationships()
  record_analytical_method()
  compare_existing_structural_assignments()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_carbohydrate_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [carbohydrate_identity, saccharide_class, residue_composition, stereochemistry, glycosidic_linkage, branching, biological_context, metabolic_context, analytical_method, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_residue_identity, preserve_stereochemistry, preserve_linkage_positions, preserve_branching, distinguish_monosaccharide_from_polysaccharide, distinguish_structure_from_function, distinguish_abundance_from_activity, distinguish_observed_from_inferred_function]
}

VALIDATE {
 REQUIRE Carbohydrate
 REQUIRE Monosaccharide
 REQUIRE GlycosidicBond
 REQUIRE Disaccharide
 REQUIRE Oligosaccharide
 REQUIRE Polysaccharide
 REQUIRE Glycan
 REQUIRE CarbohydrateMetabolism
 REQUIRE Glycosylation
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT Monosaccharide != Polysaccharide
 ASSERT stereochemical_identity REQUIRES stereochemical_context
 ASSERT glycan_structure REQUIRES linkage_context
 ASSERT abundance != 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 "CarbohydrateOntology"