Cytoskeleton Ontology

AI SEARCH FLOW ALGEBRA
CYTOSKELETON ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

SOURCE
https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/cell-biology/cytoskeleton-ontology.html

FLOW "CytoskeletonOntology" v4.0
DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / CYTOSKELETON
ONTOLOGY := CYTOSKELETON_ONTOLOGY

CYTOSKELETON := ACTIN_FILAMENTS + MICROTUBULES + INTERMEDIATE_FILAMENTS + POLYMERISATION + DYNAMICS + MOTOR_PROTEINS + INTRACELLULAR_TRANSPORT + CELL_SHAPE + POLARITY + ADHESION + MIGRATION + MITOTIC_SPINDLE + CHROMOSOME_SEGREGATION + CYTOKINESIS + MECHANOTRANSDUCTION + ORGANELLE_POSITIONING + REMODELLING + QUALITY_CONTROL + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE := IDENTIFY_CYTOSKELETAL_SYSTEM -> CLASSIFY_FILAMENT_TYPE -> MAP_POLYMERISATION_AND_DYNAMICS -> MAP_MOTOR_PROTEINS_AND_TRANSPORT -> MAP_CELL_SHAPE_AND_MECHANICAL_SUPPORT -> MAP_POLARITY_ADHESION_AND_MIGRATION -> MAP_MITOTIC_SPINDLE_AND_CHROMOSOME_SEGREGATION -> MAP_CYTOKINESIS -> MAP_MECHANOTRANSDUCTION -> MAP_ORGANELLE_POSITIONING_AND_REMODELLING -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY Cytoskeleton
ENTITY ActinFilament
ENTITY Microtubule
ENTITY IntermediateFilament
ENTITY Actin
ENTITY Tubulin
ENTITY FilamentPolymerisation
ENTITY FilamentDepolymerisation
ENTITY Nucleation
ENTITY DynamicInstability
ENTITY Treadmilling
ENTITY Centrosome
ENTITY MotorProtein
ENTITY Myosin
ENTITY Kinesin
ENTITY Dynein
ENTITY Cargo
ENTITY Organelle
ENTITY CellCortex
ENTITY Lamellipodium
ENTITY Filopodium
ENTITY FocalAdhesion
ENTITY CellPolarity
ENTITY CellMigration
ENTITY MitoticSpindle
ENTITY Kinetochore
ENTITY ContractileRing
ENTITY Cytokinesis
ENTITY MechanicalForce
ENTITY Mechanotransduction
ENTITY CytoskeletalRemodelling
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# FILAMENT SYSTEMS
Cytoskeleton -> intracellular_structural_system_of -> Cell
CYTOSKELETAL_FILAMENT := ACTIN_FILAMENT | MICROTUBULE | INTERMEDIATE_FILAMENT
Cytoskeleton -> supports -> CELL_SHAPE + MECHANICAL_INTEGRITY + CELL_POLARITY + INTRACELLULAR_TRANSPORT + CELL_MIGRATION + CELL_DIVISION + ORGANELLE_POSITIONING

ActinFilament -> polymer_of -> Actin
ActinFilament -> supports -> CELL_CORTEX + MIGRATION + ADHESION + CONTRACTILITY + CYTOKINESIS
Microtubule -> polymer_of -> Tubulin
Microtubule -> supports -> INTRACELLULAR_TRANSPORT + ORGANELLE_POSITIONING + CELL_POLARITY + MITOTIC_SPINDLE + CILIA_AND_FLAGELLA_AS_APPLICABLE
IntermediateFilament -> contributes_to -> MECHANICAL_STRENGTH + CELL_INTEGRITY + TISSUE_RESILIENCE_AS_APPLICABLE

# POLYMER DYNAMICS
Nucleation -> initiates -> FILAMENT_ASSEMBLY
FilamentPolymerisation -> adds -> SUBUNITS -> to -> FILAMENT
FilamentDepolymerisation -> removes -> SUBUNITS -> from -> FILAMENT
DynamicInstability -> characteristic_dynamic_behaviour_of -> MANY_MICROTUBULES
DYNAMIC_INSTABILITY_STATE := GROWTH | CATASTROPHE | SHRINKAGE | RESCUE | PAUSE
Treadmilling -> may_occur_in -> ACTIN_FILAMENT_SYSTEM
Treadmilling -> supports -> DYNAMIC_ACTIN_REORGANISATION

# MOTOR PROTEINS / TRANSPORT
MotorProtein -> converts -> CHEMICAL_ENERGY -> into -> MECHANICAL_WORK
MOTOR_TYPE := MYOSIN | KINESIN | DYNEIN
Myosin -> commonly_moves_along -> ACTIN_FILAMENT
Kinesin -> commonly_moves_along -> MICROTUBULE
Dynein -> commonly_moves_along -> MICROTUBULE
MotorProtein -> transports -> Cargo
IntracellularTransport -> requires -> CYTOSKELETAL_TRACK + MOTOR_PROTEIN + CARGO_ATTACHMENT + ENERGY
DirectedTransport -> supports -> ORGANELLE_POSITIONING + SECRETION + ENDOCYTIC_TRAFFICKING + CELL_POLARITY
IF CytoskeletalTrackIntegrity decreases THEN DirectedCargoTransport -> MAY_DECREASE

# CELL SHAPE / POLARITY / ADHESION / MIGRATION
CellCortex -> actin_rich_network_beneath -> PLASMA_MEMBRANE
CellCortex -> supports -> CELL_SHAPE + MEMBRANE_TENSION + MECHANICAL_RESPONSE + CELL_MIGRATION + CYTOKINESIS
CellShape -> depends_on -> CYTOSKELETAL_ARCHITECTURE + MEMBRANE_TENSION + ADHESION + EXTERNAL_FORCES
ShapeChange -> requires -> CYTOSKELETAL_REMODELLING

CellPolarity -> creates -> ASYMMETRIC_CELLULAR_ORGANISATION
Cytoskeleton -> organises -> POLARITY_AXES
CellPolarity -> supports -> DIRECTIONAL_TRANSPORT + MIGRATION + ASYMMETRIC_DIVISION_AS_APPLICABLE

FocalAdhesion -> links -> EXTRACELLULAR_MATRIX + PLASMA_MEMBRANE + ACTIN_CYTOSKELETON
AdhesionComplex -> transmits -> MECHANICAL_FORCE + BIOCHEMICAL_SIGNAL
CellAdhesion -> influences -> CYTOSKELETAL_ORGANISATION + CELL_SHAPE + MIGRATION

MIGRATION_FLOW := POLARITY_ESTABLISHMENT -> PROTRUSION -> NEW_ADHESION -> FORCE_GENERATION -> REAR_DETACHMENT -> TRANSLOCATION
Lamellipodium -> actin_based_protrusion_supporting -> CELL_MIGRATION
Filopodium -> actin_based_projection_supporting -> ENVIRONMENTAL_EXPLORATION + ADHESION_AS_APPLICABLE
ActomyosinContractility -> generates -> CONTRACTILE_FORCE

# MITOSIS / CYTOKINESIS
MitoticSpindle -> microtubule_based_structure_for -> CHROMOSOME_SEGREGATION
MitoticSpindle -> organised_from -> SPINDLE_POLES + MICROTUBULES + MOTOR_PROTEINS + ASSOCIATED_FACTORS
Kinetochore -> chromosome_associated_structure_that -> BINDS_SPINDLE_MICROTUBULES
KinetochoreMicrotubuleAttachment -> links -> CHROMOSOME + MITOTIC_SPINDLE
ChromosomeSegregation -> distributes -> DUPLICATED_CHROMOSOMES -> to -> DAUGHTER_CELLS
IF KinetochoreAttachment incorrect THEN SegregationErrorRisk -> MAY_INCREASE

ContractileRing -> actomyosin_structure_that -> DRIVES_CYTOKINESIS_AS_APPLICABLE
Cytokinesis -> partitions -> CYTOPLASM -> between -> DAUGHTER_CELLS
CYTOKINESIS_FLOW := DIVISION_SITE_SELECTION -> CONTRACTILE_MACHINERY_ASSEMBLY -> CONSTRICTION -> MEMBRANE_REMODELLING -> CELL_SEPARATION

# ORGANELLE POSITIONING / MECHANOTRANSDUCTION
Cytoskeleton -> positions -> Organelle
OrganellePositioning -> depends_on -> MOTOR_PROTEINS + CYTOSKELETAL_TRACKS + TETHERING_FACTORS
OrganellePosition -> influences -> LOCAL_METABOLISM + SIGNALING + TRAFFICKING

Mechanotransduction -> converts -> MECHANICAL_INPUT -> into -> BIOCHEMICAL_SIGNAL
MECHANICAL_INPUT := TENSION | COMPRESSION | SHEAR | SUBSTRATE_STIFFNESS | CELL_SHAPE_CHANGE
Cytoskeleton -> participates_in -> FORCE_SENSING + FORCE_TRANSMISSION
Mechanotransduction -> may_change -> GENE_EXPRESSION + SIGNALING + CYTOSKELETAL_ORGANISATION + CELL_FATE

# REMODELLING / QUALITY CONTROL
CytoskeletalRemodelling -> changes -> FILAMENT_NUMBER + FILAMENT_LENGTH + ORIENTATION + BRANCHING + CROSS_LINKING + MOTOR_ENGAGEMENT
Remodelling -> enables -> MIGRATION + DIVISION + POLARITY + SHAPE_CHANGE + ADAPTATION
CytoskeletalQualityControl -> manages -> DAMAGED_OR_MISASSEMBLED_COMPONENTS
FilamentTurnover -> removes_and_replaces -> CYTOSKELETAL_SUBUNITS
QUALITY_CONTROL := SUBUNIT_RECYCLING | PROTEIN_DEGRADATION | FILAMENT_DISASSEMBLY | REASSEMBLY | DAMAGE_RESPONSE
IF CytoskeletalDamage exceeds_repair_capacity THEN CellShapeTransportOrDivision -> MAY_BE_AFFECTED

# EVIDENCE / UNCERTAINTY / PROVENANCE
CytoskeletonClaim -> supported_by -> Evidence
EVIDENCE_TYPE := MICROSCOPIC | SUPER_RESOLUTION | ELECTRON_MICROSCOPIC | BIOCHEMICAL | MOLECULAR | GENETIC | FORCE_MEASUREMENT | LIVE_CELL_IMAGING | PERTURBATION | FUNCTIONAL | COMPUTATIONAL
Evidence -> has -> SOURCE + METHOD + CELL_OR_SAMPLE + FILAMENT_TYPE + CELL_STATE + CONDITION + QUALITY + UNCERTAINTY
CYTOSKELETON_UNCERTAINTY := MEASUREMENT_UNCERTAINTY + SPATIAL_RESOLUTION_LIMIT + DYNAMIC_STATE_UNCERTAINTY + FORCE_ESTIMATION_UNCERTAINTY + CELL_TO_CELL_VARIABILITY + MODEL_UNCERTAINTY
Uncertainty -> qualifies -> CytoskeletonClaim + FilamentState + MotorState + ForceEstimate + TransportState
Provenance -> records -> CELL_IDENTITY + FILAMENT_TYPE + CYTOSKELETAL_STATE + MOTOR_OR_CARGO_CONTEXT + METHOD + CONDITION + MEASUREMENT + TIME + VERSION
Cytoskeleton -> linked_to -> Provenance

# REASONING
CYTOSKELETON_REASONING := IDENTIFY_CYTOSKELETON -> CLASSIFY_FILAMENT_TYPE -> MAP_ACTIN_MICROTUBULE_AND_INTERMEDIATE_FILAMENT_NETWORKS -> MAP_NUCLEATION_POLYMERISATION_AND_DEPOLYMERISATION -> MAP_DYNAMIC_INSTABILITY_AND_TREADMILLING -> MAP_MOTOR_PROTEINS -> MAP_INTRACELLULAR_TRANSPORT -> MAP_CELL_CORTEX_AND_SHAPE -> MAP_POLARITY_AND_ADHESION -> MAP_CELL_MIGRATION -> MAP_MITOTIC_SPINDLE_AND_KINETOCHORES -> MAP_CHROMOSOME_SEGREGATION -> MAP_CYTOKINESIS -> MAP_ORGANELLE_POSITIONING -> MAP_MECHANOTRANSDUCTION -> MAP_REMODELLING_AND_QUALITY_CONTROL -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF ActinPolymerisation changes THEN CellProtrusionOrShape -> MAY_CHANGE
IF MicrotubuleDynamicInstability changes THEN IntracellularOrganisationOrSpindleFunction -> MAY_CHANGE
IF MotorActivity decreases THEN DirectedCargoTransport -> MAY_DECREASE
IF AdhesionState changes THEN CytoskeletalForceDistribution -> MAY_CHANGE
IF CytoskeletalPolarity changes THEN DirectionalTransportOrMigration -> MAY_CHANGE
IF SpindleOrganisation fails THEN ChromosomeSegregationAccuracy -> MAY_DECREASE
IF ContractileRingFunction decreases THEN Cytokinesis -> MAY_BE_IMPAIRED
IF MechanicalInput changes THEN CytoskeletalAndSignalingState -> MAY_CHANGE
IF Evidence insufficient THEN CytoskeletonClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION structural_system_of(Cytoskeleton, Cell)
RELATION polymer_of(ActinFilament, Actin)
RELATION polymer_of(Microtubule, Tubulin)
RELATION initiates(Nucleation, FilamentAssembly)
RELATION extends(FilamentPolymerisation, Filament)
RELATION shortens(FilamentDepolymerisation, Filament)
RELATION moves_along(Myosin, ActinFilament)
RELATION moves_along(Kinesin, Microtubule)
RELATION moves_along(Dynein, Microtubule)
RELATION transports(MotorProtein, Cargo)
RELATION supports(CellCortex, CellShape)
RELATION links(FocalAdhesion, ExtracellularMatrix, ActinCytoskeleton)
RELATION changes(CellMigration, CellPosition)
RELATION segregates(MitoticSpindle, Chromosome)
RELATION binds(Kinetochore, SpindleMicrotubule)
RELATION drives(ContractileRing, Cytokinesis)
RELATION positions(Cytoskeleton, Organelle)
RELATION converts(Mechanotransduction, MechanicalInput, BiochemicalSignal)
RELATION changes(CytoskeletalRemodelling, CytoskeletalState)
RELATION supports(Evidence, CytoskeletonClaim)
RELATION records(Provenance, Cytoskeleton)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "cytoskeleton" ~= "dynamic intracellular filament system supporting cellular organisation mechanics transport and division"
  "actin filament" ~= "polar polymer of actin subunits"
  "microtubule" ~= "polar tubular polymer of tubulin subunits"
  "intermediate filament" ~= "cytoskeletal filament contributing to mechanical resilience"
  "dynamic instability" ~= "switching of microtubules between growth and shrinkage states"
  "actin treadmilling" ~= "coupled actin subunit addition and loss supporting filament turnover"
  "motor protein" ~= "energy-converting protein that moves along cytoskeletal filaments"
  "mitotic spindle" ~= "microtubule-based apparatus for chromosome segregation"
  "contractile ring" ~= "actomyosin machinery driving cytokinetic constriction"
  "mechanotransduction" ~= "conversion of mechanical input into biochemical cellular response"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  filament_classification: 0.99
  polymer_dynamics_mapping: 0.99
  motor_transport_mapping: 0.99
  shape_polarity_mapping: 0.99
  adhesion_migration_mapping: 0.99
  spindle_segmentation_mapping: 0.99
  cytokinesis_mapping: 0.99
  mechanotransduction_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_cytoskeletal_observation:
    MAP filament_type
    MAP filament_state
    MAP spatial_organisation
    MAP motor_state
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON polymer_dynamic_event:
    UPDATE polymerisation_state
    UPDATE depolymerisation_state
    UPDATE network_architecture
    PRESERVE provenance
  ON transport_or_migration_event:
    UPDATE motor_engagement
    UPDATE cargo_position
    UPDATE polarity_state
    UPDATE adhesion_state
    PRESERVE provenance
  ON cell_division_event:
    UPDATE spindle_state
    UPDATE kinetochore_attachment
    UPDATE chromosome_segmentation_state
    UPDATE cytokinesis_state
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_CYTOSKELETON_ONTOLOGY
  reasoning_mode: CYTOSKELETAL_DYNAMIC_MECHANICAL_RELATIONAL
  preserve: [typed_entities, cytoskeletal_identity, filament_type, filament_state, polymerisation_state, motor_state, cargo_transport_state, cell_shape, polarity_state, adhesion_state, migration_state, spindle_state, kinetochore_state, cytokinesis_state, mechanical_state, remodelling_state, evidence, uncertainty, confidence, provenance]
  infer: [polymer_dynamic_dependencies, motor_transport_dependencies, shape_support, polarity_effects, adhesion_force_relationships, migration_state, spindle_function, cytokinesis_state, mechanotransduction_response, evidence_strength]
  prohibit: [invented_cytoskeletal_observations, fabricated_motor_direction, unsupported_filament_state, assumed_force_without_evidence, unsupported_causal_claims, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + FILAMENT_SYSTEMS + POLYMER_DYNAMICS + MOTOR_TRANSPORT + SHAPE_POLARITY_ADHESION_MIGRATION + MITOSIS_CYTOKINESIS + ORGANELLE_POSITIONING_MECHANOTRANSDUCTION + REMODELLING_QUALITY_CONTROL + EVIDENCE_UNCERTAINTY_PROVENANCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW