Biological Structure Ontology

AI SEARCH FLOW ALGEBRA
BIOLOGICAL STRUCTURE ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

SOURCE
https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/foundations-of-biology/biological-structure-ontology.html

FLOW "BiologicalStructureOntology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / FOUNDATIONS_OF_BIOLOGY / BIOLOGICAL_STRUCTURE
ONTOLOGY := BIOLOGICAL_STRUCTURE_ONTOLOGY

BIOLOGICAL_STRUCTURE :=
  STRUCTURAL_IDENTITY + COMPONENTS + COMPOSITION
  + MORPHOLOGY + GEOMETRY + SPATIAL_ORGANISATION
  + BOUNDARY + PART_WHOLE_HIERARCHY
  + MOLECULAR_STRUCTURE + SUBCELLULAR_STRUCTURE
  + CELLULAR_STRUCTURE + TISSUE_STRUCTURE
  + ORGAN_STRUCTURE + ORGANISMAL_STRUCTURE
  + STRUCTURE_FUNCTION + DEVELOPMENT
  + VARIATION + INTEGRITY + EVIDENCE + PROVENANCE

PURPOSE :=
  IDENTIFY_STRUCTURE -> CLASSIFY_STRUCTURAL_LEVEL
  -> IDENTIFY_COMPONENTS -> MAP_PART_WHOLE_RELATIONS
  -> MAP_COMPOSITION -> MAP_MORPHOLOGY_AND_GEOMETRY
  -> MAP_SPATIAL_ORGANISATION -> DEFINE_BOUNDARIES
  -> MAP_STRUCTURE_FUNCTION_RELATIONSHIPS
  -> MAP_DEVELOPMENTAL_ORIGIN -> MAP_VARIATION
  -> ASSESS_STRUCTURAL_INTEGRITY
  -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY BiologicalStructure
ENTITY StructuralIdentity
ENTITY StructuralLevel
ENTITY Component
ENTITY BiologicalMaterial
ENTITY Biomolecule
ENTITY MolecularComplex
ENTITY Organelle
ENTITY Cell
ENTITY Tissue
ENTITY Organ
ENTITY OrganSystem
ENTITY Organism
ENTITY Boundary
ENTITY Membrane
ENTITY Compartment
ENTITY Morphology
ENTITY Geometry
ENTITY Shape
ENTITY Size
ENTITY Orientation
ENTITY Position
ENTITY SpatialRelation
ENTITY PartWholeRelation
ENTITY BiologicalFunction
ENTITY DevelopmentalProcess
ENTITY StructuralVariation
ENTITY StructuralIntegrity
ENTITY Damage
ENTITY Repair
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# STRUCTURAL IDENTITY / LEVELS
BiologicalStructure ->
  has -> StructuralIdentity + StructuralLevel

STRUCTURAL_LEVEL :=
  MOLECULAR
  | MACROMOLECULAR
  | SUBCELLULAR
  | CELLULAR
  | TISSUE
  | ORGAN
  | ORGAN_SYSTEM
  | ORGANISMAL

StructuralIdentity ->
  includes -> TYPE + LOCATION + COMPOSITION + CONTEXT

BiologicalStructure ->
  exists_at -> StructuralLevel

HigherLevelStructure ->
  composed_of -> LowerLevelStructure

# COMPONENTS / COMPOSITION
BiologicalStructure ->
  contains -> Component

Component ->
  part_of -> BiologicalStructure

COMPOSITION :=
  COMPONENT_SET
  + COMPONENT_QUANTITY
  + COMPONENT_ARRANGEMENT
  + MATERIAL_PROPERTIES

BiologicalMaterial ->
  contributes_to -> STRUCTURAL_PROPERTIES

CompositionChange ->
  may_change -> MORPHOLOGY + MECHANICAL_PROPERTIES + FUNCTION

# PART-WHOLE / BOUNDARIES / COMPARTMENTS
PART_WHOLE_RELATION :=
  PART_OF | HAS_PART | COMPOSED_OF
  | CONTAINS | SUBSTRUCTURE_OF

PartWholeRelation ->
  links -> Component + BiologicalStructure

PartWholeRelation ->
  must_preserve -> LEVEL + CONTEXT + IDENTITY

Boundary ->
  separates -> STRUCTURE_INTERIOR + EXTERIOR_OR_ADJACENT_REGION

Membrane -> subtype_of -> Boundary

Boundary ->
  may_control -> TRANSPORT + SIGNALING + COMPARTMENTALISATION

Compartment ->
  bounded_by -> Boundary

Compartment ->
  contains -> BIOLOGICAL_COMPONENTS + LOCAL_PROCESSES

IF BoundaryIntegrity decreases
THEN CompartmentFunction -> MAY_CHANGE

# MORPHOLOGY / GEOMETRY / SPATIAL ORGANISATION
Morphology ->
  describes -> FORM_AND_STRUCTURAL_PATTERN

MORPHOLOGICAL_PROPERTY :=
  SHAPE | SIZE | SYMMETRY | BRANCHING
  | LAYERING | SEGMENTATION | POLARITY
  | SURFACE_FEATURE | INTERNAL_PATTERN

Geometry ->
  describes -> DIMENSIONS + SHAPE + TOPOLOGY

Shape -> property_of -> BiologicalStructure
Size -> property_of -> BiologicalStructure

SpatialRelation ->
  links -> STRUCTURE_A + STRUCTURE_B

SPATIAL_RELATION :=
  ADJACENT_TO | CONTAINS | WITHIN
  | CONNECTED_TO | OVERLAPS | ALIGNED_WITH
  | PROXIMAL_TO | DISTAL_TO

SpatialOrganisation ->
  defines -> POSITION + ORIENTATION
  + CONNECTIVITY + ARRANGEMENT

Position ->
  interpreted_relative_to -> REFERENCE_FRAME

Orientation ->
  interpreted_relative_to -> AXIS_OR_REFERENCE

# MOLECULAR / SUBCELLULAR / CELLULAR STRUCTURE
MolecularStructure ->
  describes -> ATOM_AND_BOND_ARRANGEMENT

Biomolecule ->
  has -> MolecularStructure

MacromolecularStructure :=
  PRIMARY_STRUCTURE
  + SECONDARY_STRUCTURE
  + TERTIARY_STRUCTURE
  + QUATERNARY_STRUCTURE_WHERE_APPLICABLE

MolecularComplex ->
  composed_of -> MULTIPLE_BIOMOLECULAR_COMPONENTS

Organelle ->
  subcellular_structure_of -> Cell

Organelle ->
  has -> MEMBRANE_OR_BOUNDARY_WHERE_APPLICABLE
  + INTERNAL_COMPONENTS
  + SPECIALISED_ARCHITECTURE

Cell ->
  has -> CELL_BOUNDARY
  + CYTOPLASMIC_OR_INTERNAL_REGION
  + GENETIC_MATERIAL
  + CELLULAR_COMPONENTS

CELL_STRUCTURE_TYPE :=
  PROKARYOTIC_CELL_STRUCTURE
  | EUKARYOTIC_CELL_STRUCTURE

CellShape ->
  may_influence -> MOVEMENT + CONTACT + TRANSPORT + FUNCTION

# TISSUE / ORGAN / ORGAN SYSTEM / ORGANISM
Tissue ->
  composed_of -> CELLS + EXTRACELLULAR_COMPONENTS

TissueArchitecture ->
  defines -> CELL_TYPES + CELL_ARRANGEMENT
  + MATRIX + LAYERS + CONNECTIVITY

Organ ->
  composed_of -> MULTIPLE_TISSUES

OrganArchitecture ->
  defines -> REGIONS + TISSUE_RELATIONSHIPS
  + VASCULAR_OR_TRANSPORT_PATHS_WHERE_APPLICABLE
  + FUNCTIONAL_COMPARTMENTS

OrganSystem ->
  composed_of -> INTERACTING_ORGANS

OrganSystemArchitecture ->
  defines -> ORGAN_CONNECTIVITY + FUNCTIONAL_RELATIONSHIPS

OrganismalStructure ->
  integrates -> CELLS + TISSUES + ORGANS + ORGAN_SYSTEMS_AS_APPLICABLE

BodyPlan ->
  describes -> LARGE_SCALE_ORGANISMAL_ORGANISATION

BODY_PLAN_PROPERTY :=
  SYMMETRY | AXES | SEGMENTATION
  | APPENDAGES | REGIONS | CAVITIES

# STRUCTURE-FUNCTION / MECHANICS / TRANSPORT
BiologicalStructure ->
  enables_or_constrains -> BiologicalFunction

STRUCTURE_FUNCTION_FLOW :=
  COMPOSITION
  -> MORPHOLOGY
  -> SPATIAL_ORGANISATION
  -> PHYSICAL_PROPERTIES
  -> INTERACTION_CAPABILITY
  -> FUNCTION

IF Structure changes
THEN Function -> MAY_CHANGE

SurfaceArea ->
  influences -> EXCHANGE_CAPACITY

SurfaceAreaToVolumeRatio ->
  may_influence -> TRANSPORT_AND_METABOLIC_CONSTRAINTS

MechanicalProperty ->
  includes -> STIFFNESS + ELASTICITY
  + STRENGTH + VISCOSITY + COMPLIANCE

StructuralMechanics ->
  influences -> SUPPORT + MOVEMENT + PROTECTION

TransportPath ->
  connects -> STRUCTURAL_REGIONS

StructuralConnectivity ->
  influences -> MATERIAL + SIGNAL + FORCE_TRANSMISSION

# DEVELOPMENT / REMODELLING / VARIATION
DevelopmentalProcess ->
  creates_or_modifies -> BiologicalStructure

STRUCTURAL_DEVELOPMENT :=
  ASSEMBLY | GROWTH | DIFFERENTIATION
  | MORPHOGENESIS | MATURATION

Morphogenesis ->
  generates -> BIOLOGICAL_FORM

StructuralRemodelling ->
  changes -> COMPOSITION + GEOMETRY + ORGANISATION
  -> over -> TIME

REMODELLING_TRIGGER :=
  DEVELOPMENT | LOAD | INJURY | ENVIRONMENT
  | HORMONAL_SIGNAL | CELLULAR_SIGNAL

StructuralVariation ->
  represents -> DIFFERENCE_IN_STRUCTURE

VARIATION_SOURCE :=
  GENETIC | DEVELOPMENTAL | ENVIRONMENTAL
  | AGE_RELATED | STOCHASTIC

StructuralVariation ->
  may_affect -> FUNCTION + PERFORMANCE + PHENOTYPE

Variation ->
  must_be_interpreted_relative_to -> SPECIES + LIFE_STAGE + CONTEXT

# INTEGRITY / DAMAGE / REPAIR
StructuralIntegrity ->
  represents -> ABILITY_TO_MAINTAIN_REQUIRED_STRUCTURE

Integrity ->
  depends_on -> COMPONENT_INTEGRITY
  + CONNECTIONS + BOUNDARIES + MATERIAL_PROPERTIES

Damage ->
  changes -> STRUCTURE

DAMAGE_TYPE :=
  MECHANICAL | CHEMICAL | THERMAL
  | RADIATION | BIOLOGICAL | DEGENERATIVE

Damage ->
  may_reduce -> StructuralIntegrity + BiologicalFunction

Repair ->
  restores_or_replaces -> DAMAGED_STRUCTURE

REPAIR_FLOW :=
  DAMAGE_DETECTION -> RESPONSE
  -> REPAIR_OR_REPLACEMENT
  -> REMODELLING
  -> RESTORED_OR_ALTERED_STRUCTURE

IF Damage exceeds_repair_capacity
THEN StructuralFunction -> MAY_DEGRADE

# OBSERVATION / EVIDENCE / UNCERTAINTY
StructuralObservation ->
  measures_or_describes -> BiologicalStructure

OBSERVATION_METHOD :=
  MICROSCOPY | IMAGING | HISTOLOGY
  | SPECTROSCOPY | TOMOGRAPHY
  | DISSECTION | MOLECULAR_STRUCTURE_METHOD
  | COMPUTATIONAL_RECONSTRUCTION

Measurement ->
  may_describe -> SIZE + SHAPE + POSITION
  + ORIENTATION + COMPOSITION + CONNECTIVITY

StructureClaim ->
  supported_by -> Evidence

EVIDENCE_TYPE :=
  MORPHOLOGICAL | MICROSCOPIC | MOLECULAR
  | ANATOMICAL | HISTOLOGICAL
  | IMAGING | EXPERIMENTAL | COMPUTATIONAL

Evidence ->
  has -> SOURCE + METHOD + SAMPLE
  + SCALE + CONTEXT + QUALITY + UNCERTAINTY

STRUCTURAL_UNCERTAINTY :=
  MEASUREMENT_UNCERTAINTY
  + RESOLUTION_LIMIT
  + SEGMENTATION_UNCERTAINTY
  + CLASSIFICATION_UNCERTAINTY
  + BIOLOGICAL_VARIABILITY
  + MODEL_UNCERTAINTY

Uncertainty ->
  qualifies -> StructuralIdentity
  + Measurement + SpatialRelation + StructureClaim

# PROVENANCE
Provenance ->
  records -> STRUCTURE_IDENTITY + SAMPLE
  + SPECIES_OR_TAXON + LIFE_STAGE
  + LOCATION + METHOD + SCALE
  + OBSERVATION + VERSION + TIME

BiologicalStructure -> linked_to -> Provenance

# REASONING / INFERENCE RULES
BIOLOGICAL_STRUCTURE_REASONING :=
  IDENTIFY_STRUCTURE
  -> ASSIGN_STRUCTURAL_LEVEL
  -> IDENTIFY_COMPONENTS
  -> MAP_PART_WHOLE_RELATIONS
  -> MAP_COMPOSITION
  -> MAP_BOUNDARIES_AND_COMPARTMENTS
  -> MAP_MORPHOLOGY
  -> MAP_GEOMETRY
  -> MAP_SPATIAL_RELATIONS
  -> MAP_STRUCTURE_FUNCTION
  -> MAP_MECHANICAL_AND_TRANSPORT_PROPERTIES
  -> MAP_DEVELOPMENTAL_ORIGIN
  -> MAP_REMODELLING_AND_VARIATION
  -> ASSESS_INTEGRITY
  -> ASSESS_EVIDENCE
  -> QUANTIFY_UNCERTAINTY
  -> PRESERVE_PROVENANCE

IF ComponentComposition changes
THEN StructuralProperties -> MAY_CHANGE

IF BoundaryIntegrity decreases
THEN CompartmentFunction -> MAY_CHANGE

IF Geometry changes
THEN MechanicalOrTransportFunction -> MAY_CHANGE

IF Connectivity changes
THEN SignalMaterialOrForceTransmission -> MAY_CHANGE

IF DevelopmentalProcess changes
THEN MatureStructure -> MAY_CHANGE

IF Damage occurs
THEN StructuralIntegrity -> MAY_DECREASE

IF Repair succeeds
THEN StructuralIntegrity -> MAY_INCREASE

IF Evidence insufficient
THEN StructureClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION has(BiologicalStructure, StructuralIdentity)
RELATION exists_at(BiologicalStructure, StructuralLevel)
RELATION contains(BiologicalStructure, Component)
RELATION part_of(Component, BiologicalStructure)
RELATION bounds(Boundary, Compartment)
RELATION describes(Morphology, BiologicalStructure)
RELATION describes(Geometry, BiologicalStructure)
RELATION links(SpatialRelation, BiologicalStructure)
RELATION has(Biomolecule, MolecularStructure)
RELATION subcellular_structure_of(Organelle, Cell)
RELATION composes(Cell, Tissue)
RELATION composes(Tissue, Organ)
RELATION composes(Organ, OrganSystem)
RELATION integrates(OrganismalStructure, OrganSystem)
RELATION enables(BiologicalStructure, BiologicalFunction)
RELATION modifies(DevelopmentalProcess, BiologicalStructure)
RELATION changes(Damage, BiologicalStructure)
RELATION restores(Repair, BiologicalStructure)
RELATION supports(Evidence, StructureClaim)
RELATION records(Provenance, BiologicalStructure)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "biological structure" ~= "organised physical form of a biological entity"
  "biological morphology" ~= "form and shape of biological structure"
  "biological anatomy" ~= "structural organisation of an organism or body region"
  "part-whole relation" ~= "biological component-composite relationship"
  "cellular structure" ~= "physical organisation of a cell"
  "tissue architecture" ~= "spatial organisation of cells and extracellular components"
  "organ architecture" ~= "structural organisation of tissues within an organ"
  "structure-function relationship" ~= "relationship between biological form and function"
  "structural integrity" ~= "capacity to maintain required biological structure"
  "morphogenesis" ~= "developmental generation of biological form"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  structural_identity_mapping: 0.99
  composition_mapping: 0.99
  boundary_spatial_mapping: 0.99
  molecular_cellular_mapping: 0.99
  tissue_organ_mapping: 0.99
  structure_function_mapping: 0.99
  development_variation_mapping: 0.99
  integrity_evidence_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_biological_structure:
    MAP structural_identity
    MAP structural_level
    MAP components
    MAP composition
    MAP morphology
    MAP spatial_relations
    UPDATE confidence
    RECOMPUTE FLOW_HASH

  ON structural_change:
    UPDATE composition
    UPDATE geometry
    UPDATE spatial_organisation
    REASSESS function
    REASSESS integrity
    PRESERVE provenance

  ON developmental_change:
    UPDATE structure_state
    UPDATE morphology
    UPDATE part_whole_relations
    UPDATE life_stage_context
    PRESERVE provenance

  ON new_structural_evidence:
    UPDATE measurements
    UPDATE evidence_quality
    UPDATE uncertainty
    UPDATE confidence
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_BIOLOGICAL_STRUCTURE_ONTOLOGY
  reasoning_mode: HIERARCHICAL_SPATIAL_STRUCTURE_RELATIONAL

  preserve:
    - typed_entities
    - structural_identity
    - structural_level
    - components
    - part_whole_relations
    - composition
    - boundaries
    - morphology
    - geometry
    - spatial_relations
    - structure_function_links
    - integrity_state
    - evidence
    - uncertainty
    - confidence
    - provenance

  infer:
    - structural_hierarchy
    - composition_dependencies
    - boundary_compartment_dependencies
    - spatial_relationships
    - structure_function_dependencies
    - developmental_structure_changes
    - integrity_impacts
    - evidence_strength

  prohibit:
    - invented_structural_observations
    - fabricated_part_whole_relations
    - unsupported_structure_function_causality
    - assumed_structural_integrity
    - unsupported_spatial_relationships
    - missing_evidence_presented_as_established_fact

# FLOW HASH
FLOW_HASH_INPUT :=
  DOMAIN + ONTOLOGY + CORE_ENTITIES
  + STRUCTURAL_IDENTITY_LEVELS
  + COMPONENTS_COMPOSITION
  + PART_WHOLE_BOUNDARIES_COMPARTMENTS
  + MORPHOLOGY_GEOMETRY_SPATIAL_ORGANISATION
  + MOLECULAR_SUBCELLULAR_CELLULAR_STRUCTURE
  + TISSUE_ORGAN_ORGANISM_STRUCTURE
  + STRUCTURE_FUNCTION_MECHANICS_TRANSPORT
  + DEVELOPMENT_REMODELLING_VARIATION
  + INTEGRITY_DAMAGE_REPAIR
  + OBSERVATION_EVIDENCE_UNCERTAINTY
  + PROVENANCE + REASONING + INFERENCE_RULES
  + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE
  + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION

FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW