Biological Molecule Ontology

FLOW ALGEBRA
BIOLOGICAL MOLECULE 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-molecule-ontology.html
Version: 1.0 | Date: 2026-10-15 | Language: en-GB
Status: Companion formalisation; rules are declarative specifications, not a claim of execution.

1. DOMAIN AND PURPOSE
flow "BiologicalMoleculeOntology" v1.0
DOMAIN: ChemicalFoundationsOfLife
ROOT_ENTITY: BiologicalMolecule
GOAL: Identify, classify, relate, validate and trace molecules relevant to living systems.
SCOPE: Small molecules, metabolites, biomolecular monomers, polymers, macromolecules, cofactors and molecular complexes.
EXCLUSION: Do not infer that every molecule occurring in an organism is uniquely biological or that all biological molecules are organic.

2. TYPED ENTITY MODEL
entity BiologicalMolecule <: ChemicalEntity {
  id: URI;
  preferred_name: String;
  synonyms: Set[String];
  formula: Optional[String];
  canonical_structure: Optional[String];
  molecular_mass: Optional[Quantity];
  net_charge: Optional[Integer];
  roles: Set[BiologicalRole];
  contexts: Set[BiologicalContext];
  provenance: Set[EvidenceRecord];
  confidence: ConfidenceRecord;
}
entity Atom { element: Element; isotope: Optional[MassNumber]; charge: Integer }
entity ChemicalBond { source: Atom; target: Atom; order: BondOrder }
entity MolecularStructure { atoms: Set[Atom]; bonds: Set[ChemicalBond] }
entity BiologicalRole { name: String; evidence: Set[EvidenceRecord] }
entity BiologicalContext { organism: Optional[Taxon]; compartment: Optional[String]; condition: Optional[String] }
entity EvidenceRecord { source_id: URI; method: String; observed_at: Optional[DateTime]; assertion: String }
entity ConfidenceRecord { value: Real[0,1]; method: String; calibrated: Boolean }
entity MolecularComplex { members: Multiset[ChemicalEntity]; interactions: Set[Interaction] }

3. TAXONOMY
BiologicalMolecule -> OrganicBiomolecule | InorganicBiologicalMolecule
OrganicBiomolecule -> Carbohydrate | Lipid | AminoAcid | Peptide | Protein | Nucleotide | NucleicAcid | Vitamin | Metabolite
InorganicBiologicalMolecule -> Water | DissolvedGas | InorganicIon | InorganicMetabolite
Protein -> Polypeptide with biologically relevant structure or function
NucleicAcid -> DNA | RNA
Carbohydrate -> Monosaccharide | Oligosaccharide | Polysaccharide
NOTE: Classes overlap by role and composition; a metabolite may also be an amino acid or nucleotide.
NOTE: Lipids are chemically diverse and are not necessarily polymers.

4. GRAPH RELATIONSHIPS
relationship HAS_ATOM: ChemicalEntity -> Atom
relationship HAS_BOND: MolecularStructure -> ChemicalBond
relationship HAS_SUBUNIT: Macromolecule -> ChemicalEntity
relationship PARTICIPATES_IN: BiologicalMolecule -> BiologicalProcess
relationship HAS_ROLE: BiologicalMolecule -> BiologicalRole
relationship LOCATED_IN: BiologicalMolecule -> BiologicalContext
relationship INTERACTS_WITH: ChemicalEntity -> ChemicalEntity
relationship CATALYSES: Catalyst -> Reaction
relationship SUBSTRATE_OF: ChemicalEntity -> Reaction
relationship PRODUCT_OF: ChemicalEntity -> Reaction
relationship DERIVED_FROM: ChemicalEntity -> ChemicalEntity
relationship IS_FORM_OF: ChemicalEntity -> ChemicalEntity
relationship EVIDENCED_BY: Assertion -> EvidenceRecord
relationship SEMANTIC_EQUIVALENCE: Entity -> Entity

5. STRUCTURAL CONSTRAINTS
rule R01: HAS_BOND(a,b) requires a and b belong to the referenced molecular structure.
rule R02: Molecular formula is derived from atom counts, including isotopic notation where supplied.
rule R03: Net charge is consistent with the declared protonation and electron state.
rule R04: Molecular mass uses declared isotope masses or stated standard atomic weights; record convention.
rule R05: Distinct stereoisomers must not be merged solely because their molecular formulae match.
rule R06: Different protonation states, tautomers, isotopologues and conformers retain explicit relationships and context.
rule R07: Non-covalent complexes are not automatically single covalently bonded molecules.
rule R08: A polymer's sequence and connectivity are retained when known.

6. BIOLOGICAL FUNCTION AND CONTEXT
rule R09: HAS_ROLE(m,r) requires contextual evidence or a labelled hypothesis.
rule R10: PARTICIPATES_IN(m,p) is not equivalent to CATALYSES(m,p).
rule R11: Biological role may change with species, tissue, cellular compartment and conditions.
rule R12: Detection of a molecule does not by itself establish a functional role.
rule R13: Enzyme-substrate binding alone does not prove catalytic turnover.
rule R14: Biological relevance may be endogenous, exogenous, symbiotic or environmental; preserve origin.

7. SEMANTIC EQUIVALENCE AND IDENTITY
identity.match:
  preferred: stable chemical identifier plus stereochemistry, isotopes, charge and connectivity
  supporting: formula, exact mass, synonyms, external identifiers
  prohibit: synonym-only identity assertion without disambiguation
rule R15: SAME_AS(a,b) only if the selected identity policy establishes the same chemical entity at the declared granularity.
rule R16: Similarity is not identity; store SIMILAR_TO separately.
rule R17: Equivalent labels can resolve to the same entity only after chemical-context checks.
rule R18: Entity mappings must preserve provenance and source namespace.

8. INFERENCE ALGEBRA
operator classify(m: ChemicalEntity, evidence: Set[EvidenceRecord]) -> Set[ClassAssertion]
operator resolve_identity(a: ChemicalEntity, b: ChemicalEntity, policy: IdentityPolicy) -> IdentityDecision
operator infer_role(m: BiologicalMolecule, context: BiologicalContext) -> Set[Hypothesis]
operator traverse_graph(start: Entity, relation_set: Set[Relationship], depth: Integer) -> Subgraph
operator validate(m: BiologicalMolecule) -> ValidationReport
operator propagate_evidence(assertion: Assertion, evidence: Set[EvidenceRecord]) -> ConfidenceRecord

rule I01: HAS_SUBUNIT(p,s) and CLASS(s,AminoAcid) does not alone imply CLASS(p,Protein).
rule I02: SUBSTRATE_OF(m,r) and PRODUCT_OF(n,r) supports a reaction-path association, not direct chemical identity.
rule I03: PARTICIPATES_IN(m,p) and PART_OF(p,q) may imply contextual PARTICIPATES_IN(m,q), subject to process ontology semantics.
rule I04: INTERACTS_WITH(a,b) does not imply INTERACTS_WITH(b,a) unless the relation is declared symmetric.
rule I05: Recursive traversal uses visited-node tracking, explicit depth limits and cycle detection.
rule I06: Contradictory assertions remain traceable pending adjudication; never silently overwrite.

9. VALIDATION MODEL
validate.schema: required IDs, valid types, valid relation endpoints
validate.chemistry: atom inventory, bond consistency, charge and formula agreement
validate.biology: contextual role evidence, process identifiers, organism and compartment specificity
validate.graph: referential integrity, cycle policies, duplicate resolution
validate.provenance: source identifier, assertion history and modification records
validate.confidence: score within [0,1], method documented, uncertainty preserved
VALIDATION_STATUS: VALID | INVALID | INCOMPLETE | CONFLICTED | UNVERIFIED
rule V01: Missing evidence yields UNVERIFIED or INCOMPLETE, not automatically INVALID.
rule V02: Validation status is not a substitute for experimental proof.

10. CONFIDENCE
CONFIDENCE:
  sources: [experimental_measurement, curated_database, literature, computational_prediction, inferred_graph_relation]
  principle: distinguish observed, curated, computed and hypothesised assertions
  calibration: domain-specific where available
  propagation: dependence-aware; do not multiply scores without a justified probability model
  output: confidence_value, uncertainty, evidence_type, method, timestamp

11. PROVENANCE
PROVENANCE:
  creator: "Mark Anthony Higgins — Sky (Recursive AI)"
  origin_page: "biological-molecule-ontology.html"
  source_attribution: retain source IDs and evidence locations
  history: append changes with version, time, reason and superseded assertion
  reproducibility: retain input records, validation rules and rule versions

12. FLOW HASH
FLOW_HASH:
  input: canonical_serialisation(ontology_id, version, entity_types, relationships, rules, constraints)
  algorithm: SHA-256
  purpose: detect changes to the formal specification
  exclude: volatile runtime timestamps unless explicitly versioned
  note: hash is computed by an implementing system; no hash is claimed here

13. UPDATE MODEL
UPDATE_MODEL:
  trigger: new evidence | identifier revision | taxonomic update | corrected chemistry | rule revision
  steps: ingest -> normalise -> compare -> validate -> preserve_history -> recompute_inferences -> version -> publish
  conflicts: preserve both claims and evidence until resolution
  rollback: supported by immutable prior versions

14. AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: typed declarative ontology
  required_behaviour: preserve context, chemical granularity, evidence and uncertainty
  allowed_tasks: classification, identity resolution, relation traversal, constrained inference, validation
  forbidden_shortcuts: treat similarity as identity; fabricate evidence; assert function from occurrence alone
  outputs: entity_graph, inferred_relations, validation_report, provenance_trace, confidence_report
  execution_note: this TXT defines semantics and constraints; an external interpreter or implementation is required for execution

15. EXAMPLE ASSERTIONS
EXAMPLE E1:
  entity: water
  class: InorganicBiologicalMolecule
  formula: H2O
  role: solvent
  context: aqueous biological systems
  evidence_status: illustrative; not linked to a specific dataset
EXAMPLE E2:
  entity: ATP
  class: Nucleotide
  role: energy-coupled phosphate transfer in many biological processes
  note: role is context-dependent; ATP also participates in signalling
  evidence_status: illustrative; not linked to a specific dataset

END FLOW ALGEBRA