Biological Boundary Ontology

FLOW ALGEBRA
Biological Boundary Ontology — Foundations of Biological Entities
Version: 1.0 | Date: 2026-10-15
Authors: Mark Anthony Higgins — Sky (Recursive AI)
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/foundations-of-biological-entities/biological-boundary-ontology.html
Status: Companion formalisation; not a verbatim extraction of hidden page code.

AI INTERPRETATION NOTE
Interpret the following as a typed, declarative reasoning specification. Do not assume an execution engine without an implementation of these operators.

flow "BiologicalBoundaryOntology" v1.0 {
  DOMAIN: Biology.EntityGraph.Foundations
  ROOT_ENTITY: BiologicalBoundary

  TYPES {
    BiologicalEntity: entity
    BiologicalBoundary: entity
    Compartment: entity
    BiologicalSystem: entity
    BiologicalProcess: process
    Material: entity
    Signal: entity
    Environment: entity
    Evidence: record
    Context: record
    TimeInterval: interval
    Confidence: real[0,1]
    ValidationResult: enum{valid,invalid,undetermined}
  }

  ENTITY BiologicalBoundary {
    id: identifier
    label: string
    boundary_kind: enum{plasma_membrane,organelle_membrane,cell_wall,
      epithelial_barrier,tissue_interface,organ_capsule,organism_surface,
      ecological_boundary,other}
    separates: tuple[Compartment,Compartment]
    associated_entity: BiologicalEntity
    physical_structure: optional[BiologicalEntity]
    permeability: optional[map[Material,ConditionDependentProperty]]
    selectivity: optional[ConditionDependentProperty]
    integrity: optional[ConditionDependentProperty]
    location: optional[Context]
    temporal_extent: optional[TimeInterval]
    evidence: set[Evidence]
    provenance: set[identifier]
    confidence: Confidence
  }

  RELATIONSHIPS {
    separates(BiologicalBoundary,Compartment,Compartment)
    bounds(BiologicalBoundary,BiologicalEntity)
    encloses(BiologicalBoundary,Compartment)
    interfaces_with(BiologicalBoundary,Environment)
    part_of(BiologicalBoundary,BiologicalSystem)
    regulates_transport(BiologicalBoundary,Material)
    permits_passage(BiologicalBoundary,Material,Context)
    restricts_passage(BiologicalBoundary,Material,Context)
    transmits_signal(BiologicalBoundary,Signal,Context)
    maintains_gradient(BiologicalBoundary,Material,Context)
    participates_in(BiologicalBoundary,BiologicalProcess)
    supported_by(BiologicalBoundary,Evidence)
  }

  AXIOMS {
    A1: every BiologicalBoundary has an associated_entity.
    A2: every separates(b,a,c) requires a != c and contextually distinguishable sides.
    A3: separates(b,a,c) does not imply impermeability.
    A4: permits_passage(b,m,c) and restricts_passage(b,m,c) may coexist
        only when they refer to different transport modes, rates or thresholds;
        otherwise mark the assertion set for contextual review.
    A5: a boundary may be dynamic, porous, selectively permeable or conceptual;
        a structural membrane is not required for every boundary kind.
    A6: part_of and bounds are not automatically interchangeable.
    A7: a biological boundary can span multiple organisation levels;
        cross-level mappings require an explicit scale and context.
  }

  RULES {
    R1: IF separates(b,a,c) AND transport_observed(m,a,c,t)
        THEN candidate(regulates_transport(b,m))
        WITH status=requires_mechanistic_evidence.
    R2: IF membrane_integrity_lost(b,t) AND evidence_supports_leakage(b,t)
        THEN infer(increased_unregulated_exchange(b,t))
        WITH context=t.
    R3: IF barrier_has_receptor(b,r) AND receptor_activated(r,s,t)
        THEN candidate(transmits_signal(b,s,t))
        WITH status=requires_pathway_validation.
    R4: IF evidence_for_separation(b,a,c) AND validated_context(a,c)
        THEN assert(separates(b,a,c)).
    R5: IF claim_conflicts_with_context(claim,context)
        THEN quarantine(claim) AND request_validation(claim).
  }

  FLOW_OPERATORS {
    IDENTIFY: observation -> candidate[BiologicalBoundary]
    CLASSIFY: candidate + context -> boundary_kind
    LINK: boundary + typed_relationship -> graph_edge
    NORMALISE: label + ontology_context -> canonical_identifier
    VALIDATE: candidate + axioms + evidence -> ValidationResult
    INFER: validated_graph + rules -> qualified_claims
    TRACE: claim -> evidence_and_rule_dependencies
    UPDATE: prior_graph + validated_changes -> versioned_graph
  }

  VALIDATION {
    V1: verify identifier uniqueness and relationship type compatibility.
    V2: verify separation endpoints and scale/context consistency.
    V3: distinguish physical boundaries from operational/ecological demarcations.
    V4: check time dependence for permeability, integrity and transport.
    V5: reject unsupported claims of universal permeability or impermeability.
    V6: check that every inferred claim retains its premises and evidence.
    V7: record undetermined rather than inventing missing observations.
  }

  SEMANTIC_EQUIVALENCE {
    canonical: BiologicalBoundary
    related_terms: [biological_barrier,biological_interface,compartment_boundary]
    exact_equivalence: only_if_same_referent_scale_function_and_context
    close_match: when_overlap_is_supported_but_identity_is_not
    non_equivalence: [BiologicalCompartment,BiologicalMembrane,BiologicalWall]
    note: a membrane or wall can instantiate a boundary but is not universally
          synonymous with the abstract boundary relation.
  }

  CONFIDENCE {
    range: [0,1]
    components: [evidence_quality,source_reliability,context_match,
                 rule_validity,independent_corroboration]
    aggregation: implementation_defined_and_calibrated
    unknown_evidence: undetermined
    propagation: do_not_increase_confidence_without_new_support
    contradictions: retain_and_flag_for_review
  }

  PROVENANCE {
    capture: [source_id,author,observation_method,timestamp,
              version,licence,context,transformation_history]
    inferred_claim: retain_premise_ids_and_rule_id
    corrections: preserve_prior_version_and_reason
  }

  FLOW_HASH {
    canonicalisation: UTF8_normalised_sorted_typed_representation
    digest: SHA256(canonicalisation)
    scope: ontology_version_plus_entity_and_relation_definitions
    note: hash is generated by an implementation; no hash is claimed here.
  }

  UPDATE_MODEL {
    input: new_evidence_or_corrected_classification
    steps: [verify_source,normalise,compare,validate,recompute_dependencies,
            preserve_history,assign_version,recalculate_hash]
    conflict_policy: preserve_competing_claims_until_resolved
  }

  AI_CONSUMPTION {
    representation: typed_entity_relationship_graph
    allowed: [classification,contextual_retrieval,qualified_inference,
              provenance_tracing,consistency_checking]
    forbidden: [fabricated_evidence,unqualified_causal_claims,
                conflation_of_boundary_and_compartment]
    output_fields: [entity_id,boundary_kind,relations,context,evidence,
                    confidence,validation_status,version,flow_hash]
  }
}

EXAMPLE GRAPH (illustrative, not a claim about a specific specimen)
entity: plasma_membrane_01 : BiologicalBoundary
separates: intracellular_space_01 | extracellular_space_01
bounds: cell_01
regulates_transport: glucose [context dependent]
validation_status: undetermined until specimen/context evidence is supplied

END FLOW ALGEBRA