Biological Object Ontology

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

PURPOSE
Represent biological objects as typed, contextualised entities in a knowledge graph, distinguishing living organisms, their components, biological products and nonliving biological materials. This is a proposed formalisation; predicates below require implementation-specific interpretation.

ENTITY TYPES
BiologicalObject <: BiologicalEntity
Organism <: BiologicalObject
Cell <: BiologicalObject
Tissue <: BiologicalObject
Organ <: BiologicalObject
Organelle <: BiologicalObject
Biomolecule <: BiologicalObject
BiologicalMaterial <: BiologicalObject
BiologicalStructure <: BiologicalObject
BiologicalSample <: BiologicalObject

ATTRIBUTES
entity_id: Identifier
canonical_label: String
entity_type: BiologicalObjectType
biological_origin: EntityID?
organisation_level: {molecular, subcellular, cellular, tissue, organ, organism, population, other}
living_status: {living, nonliving, formerly_living, unknown, not_applicable}
taxon: TaxonID?
location: SpatialReference?
time_context: TemporalReference?
state: String?
source: ProvenanceReference
confidence: Float[0,1]

RELATIONSHIP TYPES
PART_OF(BiologicalObject, BiologicalObject)
HAS_PART(BiologicalObject, BiologicalObject)
DERIVED_FROM(BiologicalObject, BiologicalObject)
PRODUCED_BY(BiologicalObject, BiologicalObject)
LOCATED_IN(BiologicalObject, SpatialEntity)
PARTICIPATES_IN(BiologicalObject, BiologicalProcess)
HAS_FUNCTION(BiologicalObject, BiologicalFunction)
INTERACTS_WITH(BiologicalObject, BiologicalObject)
INSTANCE_OF(BiologicalObject, BiologicalObjectType)
SEMANTIC_EQUIVALENCE(BiologicalObject, BiologicalObject, Context)

TYPE AND INTEGRITY CONSTRAINTS
C1: each entity_id identifies one tracked entity within its namespace.
C2: PART_OF(x,y) implies x != y; cycles in strict physical partonomy are invalid.
C3: HAS_PART(y,x) iff PART_OF(x,y), within the same asserted context.
C4: DERIVED_FROM does not imply PART_OF or living_status=living.
C5: classification as BiologicalObject does not imply the object is alive.
C6: organism membership and biological origin are distinct from taxonomic identity.
C7: temporal changes to state and living_status retain historical provenance.
C8: taxonomic assertions require a declared taxonomy and version.

FLOW OPERATORS
flow REGISTER_OBJECT(raw, context) -> BiologicalObject:
  require raw.identifier or resolvable_identity(raw, context)
  normalise identifiers, labels and source context
  assign typed object classification
  emit provenance-linked entity record

flow CLASSIFY_OBJECT(entity, evidence) -> Classification:
  assess structural level, origin, material and living status separately
  reject unsupported conflation of biological and living
  attach evidence and uncertainty to each assertion

flow LINK_OBJECTS(a, relation, b, context) -> GraphEdge:
  validate relation domain and range
  check context, time, identity and cycle constraints
  preserve assertion source and confidence
  emit validated typed edge

flow REASON_OVER_OBJECTS(graph, query) -> InferenceSet:
  select context-compatible asserted edges
  apply explicitly licensed inference rules only
  distinguish asserted, inferred and hypothetical edges
  retain proof trace and originating evidence

flow VALIDATE_OBJECT(entity, graph) -> ValidationReport:
  verify identifier, types, required provenance and confidence bounds
  inspect inconsistent living-state or partonomy claims
  flag missing taxonomic, spatial or temporal context
  return pass, warning or fail with diagnostics

INFERENCE RULES
R1: HAS_PART(y,x) => PART_OF(x,y).
R2: PART_OF(x,y) and PART_OF(y,z) => PART_OF(x,z), only when the relation is declared transitive in the applicable context.
R3: DERIVED_FROM(x,y) does not establish current membership, viability or genetic identity.
R4: SAME_AS(x,y) may merge nodes only after identity validation; semantic similarity alone is insufficient.
R5: HAS_FUNCTION(x,f) is context-dependent; no function may be inferred solely from a broad entity label.

SEMANTIC_EQUIVALENCE
Compare canonical concepts, taxonomy, level of organisation, temporal state and contextual scope. Use exact identity only when identifiers and identity criteria agree. Preserve broader-than, narrower-than and related-to links rather than collapsing distinct entities.

CONFIDENCE
Each assertion carries confidence in [0,1], method, source and review status. Confidence is not a substitute for experimental validation. Conflicting evidence is retained and flagged rather than silently overwritten.

PROVENANCE
Record source URI, retrieval or observation date, author or instrument where known, assertion method, source version, transformations, and derivation dependencies. Distinguish source assertions from proposed algebraic rules.

FLOW_HASH
Canonicalise entity IDs, typed edges, contexts, version and rule identifiers. Compute a deterministic cryptographic digest of the canonical representation. A hash identifies a representation version, not scientific truth.

UPDATE_MODEL
On source changes, revalidate affected entities and dependent edges; preserve version history, recompute affected hashes, invalidate stale inferences and emit a change log. Never overwrite contradictory evidence without a recorded resolution.

AI_CONSUMPTION
Input: typed biological objects, evidence, contexts and graph relations.
Output: grounded classifications, explainable traversals, validation results and traceable inferences.
Requirements: provenance-aware retrieval; uncertainty propagation; context-sensitive reasoning; no fabricated evidence; clear separation of observed, inferred and hypothetical claims.

EXAMPLE
entity cell_001: Cell {living_status: living, organisation_level: cellular}
entity nucleus_001: Organelle {living_status: not_applicable, organisation_level: subcellular}
edge PART_OF(nucleus_001, cell_001) [source: example, status: illustrative]
This edge expresses biological structure, not independent viability of the nucleus.

END FLOW ALGEBRA