Biological Solvent Ontology

FLOW ALGEBRA
BIOLOGICAL SOLVENT ONTOLOGY
Kireth Semantic Library | Entity Graph | Biological Entities | Chemical Foundations of Life
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/chemical-foundations-of-life/biological-solvent-ontology.html
Version: 1.0 | 2026-10-15 | Locale: en-GB
Authors: Mark Higgins — Sky (Recursive AI)
Licence: Open Research Licence — free reuse, adaptation and distribution.

PURPOSE
Represent solvents and solvent environments participating in biological systems, distinguishing chemical identity, mixture composition, phase, compartment, solvation behaviour, biological role and evidence. This is a companion formalisation, not a verbatim extraction of the source page.

TYPES
BiologicalSolvent <: ChemicalEntity
SolventSpecies <: MolecularEntity
SolventMixture <: MaterialMixture
Solute <: ChemicalEntity
Solution <: MaterialSystem
BiologicalCompartment <: BiologicalEntity
SolvationShell <: MolecularAssembly
SolventProperty <: MeasurableProperty
SolventProcess <: BiologicalProcess
Observation <: EvidenceEntity
Context <: SemanticContext

ENTITY ATTRIBUTES
entity_id: stable URI
label: string
chemical_formula: string? (species only)
composition: map[Species, Fraction]? (mixtures)
phase: {liquid, gas, solid, supercritical, unknown}
compartment_id: URI?
temperature_K: real?
pressure_Pa: real?
pH: real? (aqueous solution, defined conditions)
polarity_descriptor: string?
dielectric_constant: real?
viscosity_Pa_s: real?
water_activity: real? (relevant mixtures)
provenance_id: URI
confidence: real in [0,1]

CANONICAL INSTANCES
water: SolventSpecies; formula H2O; common dominant solvent of cells
cytosol: BiologicalCompartment; contains aqueous solvent mixture
blood_plasma: BiologicalCompartment; contains aqueous solution
lipid_membrane_core: BiologicalCompartment; hydrophobic microenvironment, not automatically a bulk liquid solvent
ethanol: SolventSpecies; can act as a solvent in experimental biological contexts

RELATIONSHIPS
SOLVATES(SolventSpecies|SolventMixture, Solute, Context)
DISSOLVED_IN(Solute, Solution)
HAS_SOLVENT(Solution, SolventSpecies|SolventMixture)
LOCATED_IN(Solution|SolventSpecies, BiologicalCompartment)
HAS_PROPERTY(SolventSpecies|SolventMixture, SolventProperty)
MODULATES(SolventProperty, SolventProcess)
PARTICIPATES_IN(SolventSpecies, BiologicalProcess)
INTERACTS_WITH(SolventSpecies, MolecularEntity)
MEASURED_BY(SolventProperty, Observation)
SUPPORTED_BY(Assertion, EvidenceEntity)

TYPE AND IDENTITY RULES
R1: HAS_SOLVENT(s,x) -> Solution(s) AND Solvent(x).
R2: DISSOLVED_IN(x,s) -> Solute(x) AND Solution(s).
R3: SOLVATES(v,x,c) -> Solvent(v) AND Solute(x) AND Context(c).
R4: SAME_CHEMICAL_IDENTITY(a,b) does not imply SAME_SOLVENT_ENVIRONMENT(a,b).
R5: Identical solvent species at different temperature, pH, ionic strength or compartment may have different biological effects.
R6: A mixture must not be equated to any one of its constituent solvent species.

CONSTRAINTS AND VALIDATION
C1: For a complete mixture composition, sum(mole_fractions) = 1 within declared tolerance.
C2: Mole fractions are each between 0 and 1.
C3: Temperature in kelvin must be greater than 0 for ordinary thermodynamic states.
C4: Property measurements require units, measurement conditions and provenance.
C5: Biological solvent claims must identify species or mixture, biological context and evidence.
C6: Do not infer solubility solely from polarity labels; use observed or appropriately modelled conditions.
C7: Distinguish solvent-mediated association from a demonstrated causal mechanism.
C8: Do not treat hydrophobic compartments as literal organic solvent phases without evidence.

FLOW OPERATORS
IDENTIFY(raw_name, context) -> CandidateSolventSet
NORMALISE(candidate, reference_vocabulary) -> CanonicalEntity
CLASSIFY(entity, context) -> TypedSolventEntity
RESOLVE_COMPOSITION(mixture, observations) -> CompositionModel
LINK(solvent, solute, compartment) -> TypedGraphEdges
EVALUATE_SOLVATION(solvent, solute, conditions) -> SolvationAssessment
VALIDATE(graph, constraints) -> ValidationReport
INFER(graph, rules, evidence) -> DerivedAssertions
TRACE(assertion) -> ProvenanceChain
UPDATE(graph, new_evidence) -> VersionedGraph
EXPORT(graph, target_schema) -> AIConsumableRepresentation

COMPOSITION
FLOW BiologicalSolventResolution(input, context):
  candidates = IDENTIFY(input.name, context)
  entity = NORMALISE(select_supported(candidates), chemical_reference)
  typed = CLASSIFY(entity, context)
  graph = LINK(typed, input.solutes, input.compartment)
  validation = VALIDATE(graph, C1..C8)
  IF validation.has_critical_errors THEN RETURN review_required(validation)
  derived = INFER(graph, R1..R6, input.evidence)
  RETURN EXPORT(attach_provenance(derived), semantic_library_schema)

SEMANTIC_EQUIVALENCE
EQUIVALENT(a,b,context) requires same canonical chemical identity or explicitly justified context-dependent mixture identity.
RELATED(a,b) does not imply EQUIVALENT(a,b).
Water, aqueous solution and cytosol are related but not interchangeable entities.
Synonyms and identifiers should be resolved against chemical reference data with provenance.

CONFIDENCE
confidence(assertion) = calibrated_score(evidence_quality, contextual_fit, method_reliability, independent_support)
Do not multiply arbitrary scores and call them calibrated probabilities.
Record evidence source, date, conditions, uncertainties and validation outcome.
Contradictory observations trigger review, not automatic deletion.

PROVENANCE
Each assertion records: assertion_id, source_id, method, timestamp, author_or_agent, context, evidence_links, confidence, validation_status, version.
Distinguish experimentally measured properties from predicted or inferred properties.

FLOW_HASH
canonical_payload = canonicalise(entity_ids, typed_edges, context, units, source_ids, schema_version)
FLOW_HASH = SHA256(UTF8(canonical_payload))
Hash is a content integrity identifier, not proof of scientific truth.

UPDATE_MODEL
On new evidence: preserve prior version; check identity and unit compatibility; recalculate affected relationships; revalidate dependent assertions; record change provenance; regenerate Flow Hash.

AI_CONSUMPTION
Provide typed entities and relations, machine-readable units, explicit contexts, evidence links, validation statuses, confidence metadata and versioned identifiers.
Disallow unsupported generalisation from experimental solvents to physiological conditions.

EXAMPLE
water --HAS_PROPERTY--> high_dielectric_permittivity [conditions specified]
cytosolic_solution --HAS_SOLVENT--> water
potassium_ion --DISSOLVED_IN--> cytosolic_solution
cytosolic_solution --LOCATED_IN--> cytosol
Each edge is an illustrative schema assertion requiring evidence for a specific instance.

END FLOW ALGEBRA