Biological Component Ontology

FLOW ALGEBRA
BIOLOGICAL COMPONENT ONTOLOGY
Kireth Semantic Library | Entity Graph | Biological Entities | Foundations
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/foundations-of-biological-entities/biological-component-ontology.html
Version: 1.0 | 2026-10-15
Authors: Mark Higgins — Sky (Recursive AI)

PURPOSE
Represent biological components as typed, context-dependent parts of biological systems, with explicit containment, composition, function, provenance and validation rules. This is a companion formalisation, not a claim that the source page specifies executable syntax.

FLOW "BiologicalComponentOntology" v1.0

ENTITY TYPES
  BiologicalEntity
  BiologicalSystem <: BiologicalEntity
  BiologicalComponent <: BiologicalEntity
  MolecularComponent <: BiologicalComponent
  CellularComponent <: BiologicalComponent
  TissueComponent <: BiologicalComponent
  OrganComponent <: BiologicalComponent
  OrganismComponent <: BiologicalComponent
  StructuralComplex <: BiologicalComponent
  BiologicalProcess
  BiologicalFunction
  BiologicalContext
  EvidenceRecord
  ProvenanceRecord

TYPED RELATIONSHIPS
  PART_OF: BiologicalComponent x BiologicalEntity -> Boolean
  HAS_PART: BiologicalEntity x BiologicalComponent -> Boolean
  COMPOSED_OF: BiologicalEntity x Set[BiologicalComponent] -> Boolean
  PARTICIPATES_IN: BiologicalComponent x BiologicalProcess -> Boolean
  CONTRIBUTES_TO: BiologicalComponent x BiologicalFunction -> Boolean
  LOCATED_IN: BiologicalComponent x BiologicalEntity -> Boolean
  INTERACTS_WITH: BiologicalComponent x BiologicalComponent -> Boolean
  DERIVED_FROM: BiologicalComponent x BiologicalEntity -> Boolean
  SUPPORTED_BY: Assertion x EvidenceRecord -> Boolean
  HAS_PROVENANCE: Assertion x ProvenanceRecord -> Boolean

AXIOMS AND CONSTRAINTS
  A1: PART_OF(c,s) => HAS_PART(s,c).
  A2: PART_OF(c,s) => BiologicalComponent(c) AND BiologicalEntity(s).
  A3: PART_OF(c,c) is false for strict parthood.
  A4: Strict PART_OF is acyclic within a single structural snapshot.
  A5: PART_OF(c,s) AND PART_OF(s,t) => PART_OF(c,t),
      only when all relations share compatible context and parthood semantics.
  A6: LOCATED_IN(c,s) does not imply PART_OF(c,s).
  A7: PARTICIPATES_IN(c,p) does not imply that c alone causes p.
  A8: Component classification is relative to a defined containing system;
      an organ can be a component of an organism and a system in its own right.
  A9: Composition and function assertions require a specified biological
      context when developmental stage, species or condition can alter them.

FLOW OPERATIONS
  REGISTER_COMPONENT(c, type, context):
    require valid_identifier(c) AND subtype(type,BiologicalComponent)
    create typed node c; attach context; preserve source evidence

  LINK_COMPONENT(c, parent, context):
    require c != parent
    require compatible_context(c,parent,context)
    require NOT creates_cycle(c,parent,context)
    assert PART_OF(c,parent) AND HAS_PART(parent,c)

  RESOLVE_COMPOSITION(parent, context):
    return validated direct components of parent within context

  TRACE_HIERARCHY(component, context):
    traverse PART_OF edges with visited-node tracking
    return paths, evidence and unresolved assertions

  INFER_FUNCTION(component, process, context):
    require supported PARTICIPATES_IN(component,process)
    infer candidate contribution only; mark as hypothesis until validated

  VALIDATE_GRAPH(graph):
    check types, identifiers, context, edge direction, cycles,
          unsupported equivalences and contradictory component claims
    return VALID | INVALID | INDETERMINATE with diagnostics

SEMANTIC EQUIVALENCE
  SEMANTIC_EQUIVALENCE(a,b,context):
    require compatible referents, granularity and biological context
    distinguish exact identity from homologous, analogous and similar parts
    return EXACT | CONTEXTUAL | RELATED | DISTINCT | UNKNOWN

CONFIDENCE
  CONFIDENCE(assertion) in [0,1]
  score may incorporate evidence quality, independent replication,
  taxonomic applicability, contextual fit and validation status
  confidence is an evidence assessment, not a proof of biological truth
  conflicting evidence must be retained, not silently overwritten

PROVENANCE
  Each assertion records source URI or identifier, author or dataset,
  observation or publication date when known, retrieval date, method,
  biological context, licence if known and revision history.

FLOW_HASH
  FLOW_HASH := SHA256(canonical_serialisation(
    ontology_version, entity_types, relationships, axioms, rules))
  Canonicalisation must define field order, encoding and normalisation.
  Hash changes signal content changes; they do not establish correctness.

UPDATE_MODEL
  on new_evidence:
    preserve prior assertions and their provenance
    reassess affected relationships and confidence
    rerun validation and dependent inference
    increment version and recompute FLOW_HASH
    publish change log

AI_CONSUMPTION
  expose typed nodes and edges with machine-readable identifiers
  expose contextual qualifiers, evidence and uncertainty
  forbid treating inferred relations as verified facts
  support graph traversal, retrieval, explanation and audit
  return UNKNOWN when evidence or context is insufficient

EXAMPLE (ILLUSTRATIVE)
  PART_OF(mitochondrion_1, cell_1)
  PART_OF(cell_1, tissue_1)
  => PART_OF(mitochondrion_1, tissue_1)
     [only under compatible structural snapshot and parthood semantics]

END FLOW