Disaccharide Ontology

FLOW ALGEBRA
DISACCHARIDE ONTOLOGY
Kireth Semantic Library | Entity Graph | Biological Entities | Macromolecular Entities
Version: 1.0 | Date: 2026-10-15 | Locale: en-GB
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/macromolecular-entities/disaccharide-ontology.html
Authorship: Mark Higgins — Sky (Recursive AI)
Research: https://kirethresearch.org

PURPOSE
Represent disaccharides as typed molecular entities, with explicit monosaccharide composition, glycosidic linkage, stereochemistry, reactions, provenance and validation. This is a companion formalisation, not a claim of machine execution or independent experimental verification.

ENTITY TYPES
Disaccharide <: Carbohydrate
Monosaccharide <: Carbohydrate
GlycosidicBond <: CovalentBond
AnomericConfiguration = {alpha, beta, unspecified}
ReducingStatus = {reducing, non_reducing, unknown}
MolecularFormula, MolecularMass, ChemicalStructure, BiologicalRole, Enzyme, Reaction, Evidence, Source, Context

ENTITY SCHEMA
entity Disaccharide {
  id: URI
  preferred_name: String
  aliases: Set[String]
  constituents: Sequence[Monosaccharide]  # exactly two residues
  linkage: GlycosidicBond
  stereochemistry: Optional[ChemicalStructure]
  molecular_formula: Optional[MolecularFormula]
  reducing_status: ReducingStatus
  roles: Set[BiologicalRole]
  provenance: Set[Evidence]
  confidence: Real[0,1]
  version: String
}

RELATIONSHIP TYPES
IS_A(Disaccharide, Carbohydrate)
HAS_RESIDUE(Disaccharide, Monosaccharide)
HAS_GLYCOSIDIC_LINKAGE(Disaccharide, GlycosidicBond)
HAS_CONFIGURATION(GlycosidicBond, AnomericConfiguration)
HAS_FORMULA(Disaccharide, MolecularFormula)
HYDROLYSES_TO(Disaccharide, Pair[Monosaccharide])
HYDROLYSED_BY(Disaccharide, Enzyme)
HAS_BIOLOGICAL_ROLE(Disaccharide, BiologicalRole)
SUPPORTED_BY(Assertion, Evidence)
SEMANTIC_EQUIVALENCE(Entity, Entity, Context)

CANONICAL INSTANCES
Sucrose: glucose residue + fructose residue; alpha-D-glucopyranosyl-(1->2)-beta-D-fructofuranoside; non-reducing.
Lactose: galactose residue + glucose residue; beta-(1->4) linkage; reducing.
Maltose: glucose residue + glucose residue; alpha-(1->4) linkage; reducing.
Trehalose: glucose residue + glucose residue; alpha,alpha-(1<->1) linkage; non-reducing.
Cellobiose: glucose residue + glucose residue; beta-(1->4) linkage; reducing.
Note: linkage descriptions assume conventional D-sugar representations and require stereochemical context for exact identity.

COMPOSITION AND REACTION ALGEBRA
For ordinary unmodified disaccharides formed by condensation of two hexoses:
  C6H12O6 + C6H12O6 - H2O -> C12H22O11
General condensation:
  mono_A + mono_B -> disaccharide + H2O
General hydrolysis:
  disaccharide + H2O -> mono_A + mono_B
The general equation is schematic; residue identity, bond topology, reaction direction and conditions must be supplied for a chemically complete model.

FLOW: IDENTIFY_DISACCHARIDE
input: molecular_structure, context, evidence
1. Parse molecular graph and stereochemical annotations.
2. Identify two sugar residues and connecting glycosidic bond.
3. Record linkage positions, anomeric configuration and ring forms.
4. Compare against curated canonical structures.
5. Distinguish exact identity from isomerism or partial similarity.
6. Attach source, confidence and unresolved fields.
output: Disaccharide | AmbiguousCandidateSet | ValidationFailure

FLOW: CLASSIFY_REDUCING_STATUS
input: validated_disaccharide_structure
rule: if a free hemiacetal/hemiketal anomeric centre remains, classify as reducing;
      if both relevant anomeric centres are locked in glycosidic acetal/ketal linkages, classify as non_reducing;
      otherwise classify as unknown.
output: status with structural justification

FLOW: HYDROLYSIS_INFERENCE
input: disaccharide, reaction_context
require: validated linkage and reaction specificity
infer: cleavage products from the two constituent residues
record: catalyst/enzyme, solvent, temperature, pH and evidence when available
output: reaction assertion, not a claim that a reaction occurred

GRAPH CONSTRAINTS
C1: A conventional disaccharide contains exactly two monosaccharide residues.
C2: Residues must be connected through a valid glycosidic linkage.
C3: Formula and atom counts must agree with explicit molecular structure.
C4: Bond positions and alpha/beta configuration must not be silently inferred from a common name when unspecified.
C5: Exact equivalence requires matching connectivity and relevant stereochemistry.
C6: Isomers and synonymous labels must be distinguished.
C7: Reducing status must follow accessible anomeric-centre chemistry.
C8: Assertions without sufficient structural or experimental evidence remain provisional.

SEMANTIC_EQUIVALENCE
exact_equivalent(a,b) iff canonicalised atom connectivity, bond order, stereochemistry and relevant protonation/tautomer context agree.
name_alias(a,b) does not alone imply exact structural equivalence.
related(a,b) may express shared constituent, class, function or hydrolysis product without identity.

CONFIDENCE
confidence(assertion) in [0,1]
Factors: source reliability, structural completeness, independent corroboration, contextual compatibility and validation outcomes.
Do not interpret heuristic confidence as an experimentally calibrated probability without calibration evidence.

PROVENANCE
Each claim carries: source_uri, author_or_organisation, retrieval_or_observation_date, method, version, evidence_type, licence_if_known.
Retain original claims alongside corrections and supersession links.

FLOW_HASH
canonical_payload = normalise(entity_type, identifiers, residues, linkage, stereochemistry, constraints, version)
FLOW_HASH = SHA256(UTF8(canonical_payload))
Exclude volatile retrieval timestamps from the stable content hash; store them in provenance metadata.

UPDATE_MODEL
on_new_evidence:
  validate(new_evidence)
  compare_with_existing_claims()
  record_conflicts_without_silent_overwrite()
  version_changed_assertions()
  recompute_affected_hashes()
  propagate_only_supported_inferences()

AI_CONSUMPTION
Provide typed entity records and edge lists; expose known/unknown fields, confidence, provenance, conflict flags and validation status. Permit machine traversal of constituent, bond, hydrolysis and biological-role relationships. Never treat an inferred relationship as an observed fact.

VALIDATION EXAMPLE
input: maltose, glucose+glucose, alpha-(1->4), reducing
checks: residue_count=2; linkage_valid=true; free_anomeric_centre=true
result: structurally consistent with canonical maltose representation.

LIMITATIONS
This flow is a declarative ontology specification. Executing the operations requires a parser, chemistry-aware graph model, canonicalisation rules and external validation datasets. Biological functions and reaction kinetics are context-dependent.

END FLOW ALGEBRA