Inorganic Biological Molecule Ontology

FLOW ALGEBRA
INORGANIC BIOLOGICAL MOLECULE ONTOLOGY
Kireth Semantic Library | Biological Entities | Chemical Foundations of Life
Version: 1.0 | Date: 2026-10-15
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/chemical-foundations-of-life/inorganic-biological-molecule-ontology.html
Authorship: Mark Higgins — Sky (Recursive AI)
Status: Companion formalisation; conceptual specification, not a verified executable runtime.

1. PURPOSE
Represent inorganic molecules and inorganic chemical species relevant to living systems, their composition, physical state, biological roles, interactions, measurements, and evidence in a typed semantic graph. Distinguish discrete molecules from monatomic ions, ionic lattices, and aqueous ionic species.

2. TYPE SYSTEM
Entity := BiologicalEntity | ChemicalEntity | Context | Observation | Evidence
ChemicalEntity := Atom | Molecule | Ion | IonicCompound | CoordinationComplex | Mixture
Molecule := InorganicMolecule | OrganicMolecule
InorganicMolecule := Water | MolecularOxygen | CarbonDioxide | Ammonia | HydrogenSulfide | NitricOxide | OtherInorganicMolecule
Ion := Cation | Anion
Context := Organism | Cell | Compartment | Environment | Process | Condition
Observation := Measurement | ExperimentalResult | LiteratureAssertion
Evidence := SourceRecord | Dataset | Protocol | InstrumentRecord

3. ENTITY ATTRIBUTES
entity_id: stable identifier
preferred_label: string
synonyms: set<string>
chemical_formula: string?
composition: map<Element, count>?
formal_charge: integer
phase: gas | liquid | solid | aqueous | unknown
structure: representation?
chemical_class: controlled term
biological_role: set<role>
organism_context: entity_id?
compartment_context: entity_id?
conditions: {temperature, pressure, pH, ionic_strength}?
provenance: set<evidence_id>
confidence: [0,1]?
validation_status: validated | provisional | disputed | rejected

4. TYPED RELATIONSHIPS
COMPOSED_OF(Molecule, Atom)
HAS_FORMULA(ChemicalEntity, Formula)
HAS_CHARGE(ChemicalEntity, Integer)
DISSOCIATES_IN(IonicCompound, Solvent)
PRODUCES_SPECIES(Process, ChemicalEntity)
CONSUMES_SPECIES(Process, ChemicalEntity)
PARTICIPATES_IN(ChemicalEntity, Process)
TRANSPORTED_ACROSS(ChemicalEntity, Boundary)
PRESENT_IN(ChemicalEntity, Compartment)
REGULATES(ChemicalEntity, BiologicalProcess)
INTERACTS_WITH(ChemicalEntity, ChemicalEntity)
MEASURED_BY(ChemicalEntity, Measurement)
SUPPORTED_BY(Assertion, Evidence)
SEMANTIC_EQUIVALENCE(Entity, Entity, Context)

5. CANONICAL INSTANCES
H2O: water; neutral molecular species; solvent and reactant.
O2: molecular oxygen; neutral diatomic species; aerobic respiration context.
CO2: carbon dioxide; neutral molecular species; respiration and carbonate chemistry.
NH3: ammonia; neutral molecule; acid-base equilibrium with NH4+.
H2S: hydrogen sulfide; neutral molecule; equilibrium with HS-.
NO: nitric oxide; neutral radical molecule; signalling in suitable contexts.
Na+: sodium ion; inorganic biological species but NOT a molecule.
K+: potassium ion; inorganic biological species but NOT a molecule.
Ca2+: calcium ion; inorganic biological species but NOT a molecule.
Cl-: chloride ion; inorganic biological species but NOT a molecule.
HCO3-: bicarbonate ion; polyatomic inorganic ion, not a neutral molecule.
PO4^3-: phosphate ion; polyatomic inorganic ion.

6. FLOW OPERATORS
REGISTER(e: ChemicalEntity) -> EntityID
CLASSIFY(e, taxonomy, context) -> ClassAssertion
NORMALISE_FORMULA(formula) -> CanonicalFormula
LINK(e1, relation, e2, evidence) -> GraphEdge
TRACE_REACTION(process, reactants, products) -> ReactionGraph
CHECK_BALANCE(reaction) -> {atom_balance, charge_balance}
RESOLVE_SPECIES(label, phase, pH, context) -> CandidateSet
VALIDATE(assertion, evidence, constraints) -> ValidationResult
INFER(graph, rules, context) -> QualifiedAssertions
EXPORT(graph, format) -> SerialisedGraph

7. VALIDATION CONSTRAINTS
C1: Every registered chemical entity has a stable identifier and a declared type.
C2: Formula parsing must conserve element identity and stoichiometric counts.
C3: Reaction balance requires equal counts of each element on both sides.
C4: Reaction charge balance requires equal net charge on both sides.
C5: Aqueous speciation claims must identify relevant pH and conditions where needed.
C6: An ion must not be silently retyped as a neutral molecule.
C7: A chemical compound must not be assumed to exist as discrete molecules in every phase.
C8: Biological function claims require a context and supporting evidence.
C9: Correlation must not be promoted to causation without appropriate evidence.
C10: Conflicting claims remain traceable rather than overwritten.

8. INFERENCE RULES
R1: IF PARTICIPATES_IN(x,p) AND TYPE(p,BiologicalProcess) THEN BiologicalParticipant(x,p), conditional on validated edges.
R2: IF PRESENT_IN(x,c) AND PART_OF(c,o) THEN ASSOCIATED_WITH_ORGANISM(x,o); do not infer universal presence.
R3: IF REACTION_BALANCED(r) AND SUPPORTED_BY(r,e) THEN ELIGIBLE_FOR_STOICHIOMETRIC_REASONING(r); balance alone does not establish kinetics or feasibility.
R4: IF HAS_FORMULA(x,f) AND HAS_FORMULA(y,f) THEN FORMULA_MATCH(x,y); do not infer identity without structure, charge, phase and context.
R5: IF REACTANT_OF(x,p) AND PRODUCT_OF(y,p) THEN CONNECTED_BY_TRANSFORMATION(x,y,p); do not infer direct causation without mechanism.

9. SEMANTIC EQUIVALENCE
Identity requires compatible chemical structure, charge, isotope specification and relevant phase/context. Synonyms may refer to one entity; identical formulas may refer to distinct isomers or species. Biological-role similarity does not imply chemical identity.

10. CONFIDENCE
CONFIDENCE(assertion) := calibrated evidence assessment in [0,1], when available.
Keep separate: source reliability, measurement uncertainty, model uncertainty, contextual applicability and logical validation. Never interpret an arbitrary score as a probability without calibration.

11. PROVENANCE
Record source URI or identifier, contributor, publication or observation date, method, dataset version, transformation lineage, and licence where known. Preserve prior revisions and rejected assertions for audit.

12. FLOW_HASH
FLOW_HASH := SHA256(canonical_serialisation(ontology_id, version, entities, relationships, rules, constraints))
Canonicalisation must fix ordering, Unicode normalisation, field encoding and excluded volatile metadata. Hash identifies a snapshot; it does not prove scientific truth.

13. UPDATE_MODEL
INPUT: proposed entities, revised observations, corrected chemical definitions.
STEPS: parse -> normalise -> type-check -> validate -> compare -> flag conflicts -> review -> version -> rehash -> publish.
OUTPUT: new version, change log, provenance graph, unresolved-conflict register.

14. AI_CONSUMPTION
Expose typed identifiers, explicit context, unit-aware measurements, qualified assertions, evidence links, confidence and validation states. AI systems must distinguish experimentally supported knowledge from inferred hypotheses, and must not substitute a text similarity match for chemical identity.

15. EXAMPLE EXECUTION
REGISTER(H2O: InorganicMolecule)
REGISTER(O2: InorganicMolecule)
REGISTER(CO2: InorganicMolecule)
REGISTER(Respiration: BiologicalProcess)
LINK(O2, PARTICIPATES_IN, Respiration, evidence_ref)
LINK(CO2, PRODUCES_SPECIES_IN, Respiration, evidence_ref)
VALIDATE(Respiration, evidence_ref, biological_context)
RESULT: a context-qualified graph; not a universal claim about all organisms or metabolic processes.

16. LIMITATIONS
This ontology is a research-oriented semantic formalisation. It is not a complete chemical database, a validated biochemical simulation, or an executable interpreter. Chemical speciation and biological effects require condition-specific experimental evidence.

END FLOW ALGEBRA