Biological Gas Ontology

FLOW ALGEBRA
BIOLOGICAL GAS ONTOLOGY
Kireth Semantic Library | Chemical Foundations of Life
Authors: Mark Anthony Higgins — Sky (Recursive AI)
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/chemical-foundations-of-life/biological-gas-ontology.html
Version: 1.0 | 2026-10-15 | Locale: en-GB

AI INTERPRETATION NOTE
Formal, typed declarative reasoning specification. The rules define intended semantics; implementation requires a conforming inference and validation engine. Do not treat a rule as empirical proof.

flow "BiologicalGasOntology" v1.0

# 01 — DOMAIN AND TYPES
ontology.id: biological_gas
ontology.parent: chemical_foundations_of_life
ontology.scope: gas species and gas-related states, transport and biological effects

type Entity = BiologicalGas | Molecule | Ion | Organism | Cell | Tissue | Compartment | Process | Reaction | Protein | Measurement | Evidence

type BiologicalGas <: Molecule
  fields:
    id: iri
    label: string
    formula: string
    chemical_identity: iri
    biological_role: set<Role>
    physical_state: StateContext
    source: Evidence?

type Role = RespiratorySubstrate | MetabolicProduct | SignallingMediator | EnvironmentalExposure | Toxicant | OtherRole

type StateContext:
  temperature_K: real?
  pressure_Pa: real?
  medium: GasPhase | Aqueous | Blood | Tissue | Other

type Measurement:
  quantity: Concentration | PartialPressure | Flux | Solubility | Saturation | ExposureDuration
  value: real
  unit: string
  location: iri?
  time: timestamp?
  method: string?
  uncertainty: real?

# 02 — EXEMPLAR ENTITIES (NOT EXHAUSTIVE)
entity O2: BiologicalGas {label:"Oxygen", formula:"O2", biological_role:[RespiratorySubstrate]}
entity CO2: BiologicalGas {label:"Carbon dioxide", formula:"CO2", biological_role:[MetabolicProduct]}
entity NO: BiologicalGas {label:"Nitric oxide", formula:"NO", biological_role:[SignallingMediator]}
entity CO: BiologicalGas {label:"Carbon monoxide", formula:"CO", biological_role:[SignallingMediator,Toxicant]}
entity H2S: BiologicalGas {label:"Hydrogen sulphide", formula:"H2S", biological_role:[SignallingMediator,Toxicant]}
entity N2: BiologicalGas {label:"Nitrogen", formula:"N2", biological_role:[EnvironmentalExposure]}

# 03 — RELATIONSHIPS
relation participates_in(BiologicalGas, Process)
relation produced_by(BiologicalGas, Process)
relation consumed_by(BiologicalGas, Process)
relation diffuses_between(BiologicalGas, Compartment, Compartment)
relation transported_by(BiologicalGas, Protein)
relation binds_to(BiologicalGas, Protein)
relation signals_through(BiologicalGas, Process)
relation measured_in(BiologicalGas, Compartment)
relation affects(BiologicalGas, Entity)
relation has_measurement(BiologicalGas, Measurement)
relation supported_by(Entity, Evidence)
relation context_of(Entity, StateContext)
relation semantically_equivalent_to(Entity, Entity)

# 04 — BIOLOGICAL PROCESSES
process CellularRespiration:
  inputs: [O2]  # aerobic respiration context
  outputs: [CO2] # typical carbon oxidation context
  caveat: reaction stoichiometry depends on substrate and organism

process GasExchange:
  participants: [O2, CO2]
  mechanisms: [diffusion, ventilation, perfusion]
  caveat: mechanisms and direction depend on organism and gradient

process GasSignalling:
  participants: [NO, CO, H2S]
  caveat: signalling depends on dose, site, mechanism and biological context

# 05 — INFERENCE RULES
rule R01_GAS_PARTICIPATION:
  when participates_in(g:BiologicalGas, p:Process)
  then classify(g, BiologicalGas); link(g,p)

rule R02_TRANSPORT:
  when transported_by(g:BiologicalGas, carrier:Protein)
  then link(g,carrier,transported_by)
  require evidence_for(g,carrier)

rule R03_DIFFUSION_DIRECTION:
  when partial_pressure(g, compartment_a, pa) and partial_pressure(g, compartment_b, pb)
       and pa > pb and membrane_permeable_to(g, compartment_a, compartment_b)
  then infer_possible_net_diffusion(g, compartment_a, compartment_b)
  note: gradient alone does not establish actual flux magnitude

rule R04_ROLE_CONTEXT:
  when has_role(g, role, context)
  then assert_role(g,role,context)
  prohibit: infer universal role without context

rule R05_TOXICITY:
  when measured_exposure(g, dose, duration, organism) and validated_threshold(g, organism, context, threshold)
  then assess_exposure_against_threshold(g,dose,duration,threshold)
  prohibit: conclude toxicity from gas identity alone

rule R06_REACTION_BALANCE:
  when reaction_has_species(r, reactants, products)
  then require atom_balance(r) and charge_balance(r)

# 06 — CONSTRAINTS AND VALIDATION
constraint V01: every gas entity has stable id, label and chemical formula
constraint V02: chemical identity must distinguish molecules from ions and radicals
constraint V03: measurements require dimensionally compatible units
constraint V04: partial pressure and concentration are distinct quantities
constraint V05: no inference of causality from co-occurrence alone
constraint V06: biological roles must be scoped by organism, compartment or conditions where relevant
constraint V07: toxicity assertions require dose, exposure route, duration and evidence where available
constraint V08: uncertain or disputed claims remain qualified, not promoted to facts
constraint V09: state-dependent gas behaviour records temperature, pressure and medium when material
constraint V10: reaction assertions pass mass and charge conservation checks

# 07 — SEMANTIC EQUIVALENCE
semantic_equivalence:
  exact_identity: canonical chemical identifier and compatible molecular form
  lexical_alias: e.g. "carbon dioxide" <=> "CO2" only within unambiguous chemical context
  non_equivalence:
    - NO != NO2
    - CO != CO2
    - dissolved_gas_concentration != gas_partial_pressure
    - molecular_oxygen_O2 != atomic_oxygen_O
  policy: never merge different species on similar names or biological roles

# 08 — PROVENANCE
provenance:
  claim_id: iri
  evidence_source: uri | citation
  evidence_type: Experimental | Observational | CuratedDatabase | Review | Derived
  method: string?
  organism: iri?
  context: string?
  observed_at: timestamp?
  retrieved_at: timestamp?
  version: string
  attribution: string

# 09 — CONFIDENCE
confidence:
  range: [0.0, 1.0]
  dimensions: [source_reliability, measurement_quality, reproducibility, context_fit, inference_validity]
  aggregation: calibrated_model_required
  policy:
    - record uncertainty and supporting evidence for each claim
    - do not interpret an uncalibrated score as probability of truth
    - derived confidence cannot exceed the strength justified by premises and inference rule
    - contradictory evidence triggers review rather than silent overwrite

# 10 — FLOW HASH
flow_hash:
  algorithm: SHA-256
  input: canonical_serialisation(ontology_id, version, entities, relations, rules, constraints)
  output: lowercase_hex_digest
  note: hash is integrity metadata, not scientific validation

# 11 — UPDATE MODEL
update_model:
  event_types: [AddEntity, ReviseClaim, AddEvidence, DeprecateAlias, UpdateMeasurement, CorrectRule]
  on_change:
    - validate types and constraints
    - preserve previous version and provenance
    - recompute affected inference dependencies
    - flag contradictions and unresolved evidence
    - regenerate flow_hash
    - publish versioned change record

# 12 — AI CONSUMPTION
ai_consumption:
  ingest: [typed_entities, relations, contextual_claims, evidence, validation_rules]
  query_modes: [classification, graph_traversal, process_lookup, evidence_lookup, qualified_inference]
  outputs: [answer, supporting_claims, provenance, confidence_status, uncertainty, ontology_version]
  safeguards:
    - separate observation from inference
    - cite source for factual claims
    - disclose unknown or missing context
    - do not fabricate measurements, mechanisms or thresholds
    - never treat this ontology as clinical guidance

# 13 — EXAMPLE QUERY FLOW
query: "Which gases participate in aerobic cellular respiration?"
resolve(Process:CellularRespiration)
traverse(inputs, outputs)
return:
  - O2: common respiratory substrate
  - CO2: common product of carbon oxidation
qualify: depends on organism, pathway and substrate
attach: provenance, context, confidence_status

# 14 — ACCEPTANCE TESTS
test T01: parse(O2) => BiologicalGas
test T02: equivalence("carbon dioxide", "CO2") => true when context unambiguous
test T03: equivalence("CO", "CO2") => false
test T04: compare(10 kPa, 100 mmol/L) => reject without conversion model
test T05: toxicity(CO, unspecified_dose) => insufficient_context
test T06: changed_claim => updated_provenance_and_hash
test T07: unsupported_causal_assertion => reject_or_qualify

END FLOW ALGEBRA