Water Molecule Ontology

FLOW ALGEBRA
WATER MOLECULE ONTOLOGY
Kireth Semantic Library — Biological Entities / Chemical Foundations of Life
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/chemical-foundations-of-life/water-molecule-ontology.html
Version: 1.0 | 2026-10-15 | Locale: en-GB
Authors: Mark Higgins — Sky (Recursive AI)
Status: Companion formalisation; conceptual specification, not an independently verified executable engine.

1. PURPOSE
Represent water molecules as chemically defined entities and connect molecular structure, phase, hydrogen bonding, solvent behaviour, transport, and biological roles to an evidence-aware semantic graph.

2. TYPE SYSTEM
ENTITY WaterMolecule <: InorganicMolecule
ENTITY HydrogenAtom <: Atom
ENTITY OxygenAtom <: Atom
ENTITY CovalentBond <: ChemicalBond
ENTITY HydrogenBond <: IntermolecularInteraction
ENTITY WaterCluster <: MolecularAssembly
ENTITY HydrationShell <: MolecularAssembly
ENTITY AqueousSolution <: Mixture
ENTITY Solute <: ChemicalEntity
ENTITY BiologicalCompartment <: BiologicalStructure
ENTITY WaterTransportProcess <: BiologicalProcess
ENTITY WaterProperty <: PhysicochemicalProperty
ENTITY Measurement <: EvidenceEntity
ENTITY SourceRecord <: ProvenanceEntity

3. CANONICAL IDENTITY
WaterMolecule.formula = H2O
WaterMolecule.atom_count = 3
WaterMolecule.composition = {H:2, O:1}
WaterMolecule.net_charge = 0
WaterMolecule.geometry = bent
WaterMolecule.phase = context_dependent
WaterMolecule.identity_scope = molecular_species

4. TYPED RELATIONSHIPS
HAS_ATOM(WaterMolecule, HydrogenAtom) [multiplicity=2]
HAS_ATOM(WaterMolecule, OxygenAtom) [multiplicity=1]
HAS_BOND(WaterMolecule, CovalentBond) [O-H, multiplicity=2]
CAN_DONATE_H_BOND(WaterMolecule, HydrogenBond)
CAN_ACCEPT_H_BOND(WaterMolecule, HydrogenBond)
PARTICIPATES_IN(WaterMolecule, HydrationShell)
IS_COMPONENT_OF(WaterMolecule, AqueousSolution)
INTERACTS_WITH(WaterMolecule, Solute)
OCCURS_IN(WaterMolecule, BiologicalCompartment)
PARTICIPATES_IN(WaterMolecule, WaterTransportProcess)
HAS_PROPERTY(WaterMolecule, WaterProperty)
SUPPORTED_BY(Assertion, SourceRecord)

5. STRUCTURAL AND PHYSICAL CONSTRAINTS
RULE composition_valid(w):
  w.type == WaterMolecule => count(H,w)==2 AND count(O,w)==1
RULE bond_valid(w):
  w.type == WaterMolecule => count_covalent_bonds(O-H,w)==2
RULE neutral_water(w):
  w.type == WaterMolecule => formal_net_charge(w)==0
RULE state_context(w,c):
  phase(w,c) must be evaluated from temperature, pressure and local environment;
  do not infer bulk phase from molecular identity alone.
RULE distinction:
  HydrogenBond != CovalentBond
  HydroniumIon != WaterMolecule
  HydroxideIon != WaterMolecule

6. BIOLOGICAL FUNCTIONS
FLOW hydration:
  INPUT WaterMolecule + Solute + Environment
  CHECK chemical_compatibility AND conditions
  DERIVE candidate HydrationShell
  OUTPUT contextualised interaction assertion

FLOW osmosis:
  INPUT WaterTransportProcess + Membrane + SoluteActivities
  CHECK membrane_permeability AND chemical_potential_gradient
  DERIVE predicted_water_flux_direction
  OUTPUT transport hypothesis with assumptions

FLOW reaction_participation:
  INPUT Reaction + WaterMolecule
  CLASSIFY water_role AS reactant | product | solvent | catalyst_environment
  CHECK atom_and_charge_balance
  OUTPUT reaction_role assertion

7. SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  'water molecule' <=> 'H2O molecule' [chemical_species_context]
  'water' ~= 'H2O' [context_required; bulk substance vs individual molecule]
  'heavy water' != 'ordinary isotopic composition water' [isotopic distinction]
  'hydronium' != 'water molecule'
RESOLUTION: match chemical formula, isotope specification, charge, entity granularity and context before merging nodes.

8. INFERENCE RULES
INFER biological_solvent_role(w,context)
  IF w:WaterMolecule AND context:aqueous_biological_environment
  THEN MAY_SUPPORT(solute_dissolution)
  WITH evidence_required=true

INFER hydrogen_bond_network(w,neighbours)
  IF compatible_geometry(w,neighbours) AND compatible_conditions
  THEN POSSIBLE_INTERMOLECULAR_NETWORK
  NOT a guaranteed bond configuration.

INFER conservation(reaction)
  IF reaction_is_balanced(reaction)
  THEN atom_inventory_preserved AND total_charge_preserved.

9. VALIDATION
VALIDATE formula == H2O
VALIDATE molecular_atom_counts == {H:2,O:1}
VALIDATE chemical_charge_consistency
VALIDATE typed_edges_and_cardinality
VALIDATE distinction_between_bulk_and_molecular_properties
VALIDATE reaction_atom_and_charge_balance
VALIDATE unit_consistency_for_temperature_pressure_concentration
VALIDATE provenance_for_empirical_claims
VALIDATE no_unsupported_causal_or_biological_inference

10. CONFIDENCE
CONFIDENCE(assertion) = calibrated_score(evidence_quality, source_reliability,
  measurement_uncertainty, model_assumptions, contextual_fit)
CONFIDENCE range: [0,1]
CONFIDENCE must not substitute for proof or empirical measurement.
Unverified claims remain explicitly unverified.

11. PROVENANCE
PROVENANCE:
  source_url: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/chemical-foundations-of-life/water-molecule-ontology.html
  source_version: unspecified
  generated_date: 2026-10-15
  evidence: attach source identifiers, measurement methods, timestamps and revisions
  authorship: Mark Higgins — Sky (Recursive AI)

12. FLOW HASH
FLOW_HASH:
  algorithm: SHA-256
  input: canonical_utf8(serialised_ontology_without_hash_field)
  output: computed_at_publish_time
  rule: never assert a digest without calculating it

13. UPDATE MODEL
UPDATE_MODEL:
  version: 1.0
  triggers: corrected chemistry | new validated evidence | schema revision
  operations: add | revise | deprecate | link | revalidate
  requirements: preserve history; record changed assertions; rerun constraints;
                recalculate Flow Hash; flag dependent inferences.

14. AI CONSUMPTION
AI_CONSUMPTION:
  parse: typed_entities + typed_edges + constraints + provenance
  reason: distinguish chemical identity from environmental behaviour
  retrieve: molecule | hydrogen bonding | hydration | osmosis | reactions
  verify: require evidence for empirical and context-specific conclusions
  emit: assertions with assumptions, uncertainty, source and validation state
  safeguard: no fabricated measurements, sources or proof status

15. EXECUTION OUTLINE
FLOW WaterMoleculeGraph(query, context):
  entities = RESOLVE(query, context)
  graph = EXPAND_TYPED_RELATIONSHIPS(entities)
  graph = APPLY_CONTEXT(graph, context)
  candidates = APPLY_INFERENCE_RULES(graph)
  validated = VALIDATE(candidates, chemical_constraints, evidence)
  annotated = ATTACH_PROVENANCE_AND_CONFIDENCE(validated)
  RETURN SERIALISE(annotated, ai_consumption_schema)

END FLOW ALGEBRA