Cell Division Ontology

AI SEARCH FLOW ALGEBRA
CELL DIVISION ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

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

FLOW "CellDivisionOntology" v4.0
DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / CELL_DIVISION
ONTOLOGY := CELL_DIVISION_ONTOLOGY

CELL_DIVISION := DIVISION_IDENTITY + CELL_CYCLE_CONTEXT + DIVISION_COMMITMENT + DNA_REPLICATION_COORDINATION + CHROMOSOME_CONDENSATION + MITOSIS + MEIOSIS + SPINDLE_ASSEMBLY + KINETOCHORE_ATTACHMENT + CHROMOSOME_SEGREGATION + CHECKPOINTS + CYTOKINESIS + DIVISION_ORIENTATION + ASYMMETRIC_DIVISION + DAUGHTER_CELL_FORMATION + DIVISION_ERRORS + QUALITY_CONTROL + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE := IDENTIFY_CELL_DIVISION_EVENT -> CLASSIFY_DIVISION_TYPE -> MAP_CELL_CYCLE_CONTEXT -> MAP_DNA_REPLICATION_COORDINATION -> MAP_CHROMOSOME_STATE -> MAP_SPINDLE_AND_KINETOCHORE_DYNAMICS -> MAP_CHROMOSOME_SEGREGATION -> MAP_CHECKPOINT_CONTROL -> MAP_CYTOKINESIS -> MAP_DIVISION_ORIENTATION_AND_ASYMMETRY -> MAP_DAUGHTER_CELL_OUTCOMES -> MAP_DIVISION_ERRORS -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY CellDivision
ENTITY CellCycle
ENTITY DivisionCommitment
ENTITY DNAReplication
ENTITY Chromosome
ENTITY SisterChromatid
ENTITY HomologousChromosome
ENTITY ChromosomeCondensation
ENTITY Centrosome
ENTITY MitoticSpindle
ENTITY SpindleMicrotubule
ENTITY Kinetochore
ENTITY Cohesin
ENTITY Separase
ENTITY Checkpoint
ENTITY SpindleAssemblyCheckpoint
ENTITY Mitosis
ENTITY Meiosis
ENTITY Cytokinesis
ENTITY ContractileRing
ENTITY CleavageFurrow
ENTITY CellPlate
ENTITY DivisionPlane
ENTITY CellPolarity
ENTITY AsymmetricCellDivision
ENTITY DaughterCell
ENTITY Aneuploidy
ENTITY CytokinesisFailure
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# CELL CYCLE / REPLICATION
CellDivision -> biological_process_that -> PRODUCES_DAUGHTER_CELLS
DIVISION_TYPE := MITOTIC_DIVISION | MEIOTIC_DIVISION | BINARY_FISSION_AS_APPLICABLE | OTHER_CELL_DIVISION_MODE
CellDivision -> coordinates -> GENOME_DISTRIBUTION + CYTOPLASMIC_PARTITIONING
CellCycle -> coordinates -> CELL_GROWTH + DNA_REPLICATION + CHROMOSOME_SEGREGATION + CELL_DIVISION
CELL_CYCLE_PHASE := G1 | S | G2 | M | G0_AS_APPLICABLE
DivisionCommitment -> depends_on -> CELL_SIZE_OR_GROWTH_STATE + NUTRIENT_STATE + SIGNALING + DNA_INTEGRITY + DEVELOPMENTAL_CONTEXT
DNAReplication -> duplicates -> GENETIC_MATERIAL -> before -> CHROMOSOME_SEGREGATION_AS_APPLICABLE
SisterChromatid -> product_of -> CHROMOSOME_REPLICATION_AS_DEFINED
SisterChromatidCohesion -> maintains -> ASSOCIATION_BETWEEN_REPLICATED_CHROMATIDS
IF DNAReplication incomplete THEN DivisionProgression -> MAY_DELAY_OR_ARREST

# MITOSIS / MEIOSIS
ChromosomeCondensation -> compacts -> CHROMATIN -> for -> SEGREGATION
MITOTIC_STAGE := PROPHASE | PROMETAPHASE | METAPHASE | ANAPHASE | TELOPHASE
MITOSIS_FLOW := CHROMOSOME_CONDENSATION -> SPINDLE_ASSEMBLY -> KINETOCHORE_ATTACHMENT -> CHROMOSOME_ALIGNMENT -> SISTER_CHROMATID_SEPARATION -> CHROMOSOME_SEGREGATION -> NUCLEAR_REORGANISATION
Mitosis -> generally_preserves -> CHROMOSOME_COMPLEMENT_AS_DEFINED

MEIOSIS := MEIOSIS_I + MEIOSIS_II
MeiosisI -> segregates -> HOMOLOGOUS_CHROMOSOMES
MeiosisII -> segregates -> SISTER_CHROMATIDS_AS_DEFINED
HomologousChromosomePairing -> supports -> RECOMBINATION + MEIOTIC_SEGREGATION
Meiosis -> contributes_to -> REDUCTION_OF_CHROMOSOME_NUMBER + GENETIC_VARIATION

# SPINDLE / KINETOCHORE
MitoticSpindle -> microtubule_based_apparatus_for -> CHROMOSOME_SEGREGATION
Centrosome -> may_function_as -> SPINDLE_POLE_ORGANISING_CENTRE_AS_APPLICABLE
SPINDLE_MICROTUBULE_TYPE := KINETOCHORE_MICROTUBULE | INTERPOLAR_MICROTUBULE | ASTRAL_MICROTUBULE_AS_APPLICABLE
Kinetochore -> chromosome_associated_structure_that -> INTERACTS_WITH_SPINDLE_MICROTUBULES
KinetochoreAttachment -> links -> CHROMOSOME + SPINDLE
AttachmentState := UNATTACHED | MONOTELIC | SYNTELIC | MEROTELIC | BIORIENTED_AS_APPLICABLE
Biorientation -> supports -> ACCURATE_CHROMOSOME_SEGREGATION
IF AttachmentError persists THEN MissegregationRisk -> MAY_INCREASE

# CHECKPOINT / SEGREGATION
SpindleAssemblyCheckpoint -> monitors -> KINETOCHORE_ATTACHMENT + CHROMOSOME_BIORIENTATION_AS_DEFINED
CheckpointUnsatisfied -> inhibits_or_delays -> ANAPHASE_ONSET
CheckpointSatisfied -> permits -> ANAPHASE_TRANSITION
Cohesin -> maintains -> SISTER_CHROMATID_COHESION
Separase -> promotes -> COHESION_RELEASE_AS_DEFINED
AnaphaseOnset -> triggers -> SISTER_CHROMATID_SEPARATION_IN_MITOSIS
ChromosomeSegregation -> distributes -> GENETIC_MATERIAL -> between -> DAUGHTER_CELL_DESTINATIONS
IF ChromosomeMissegregation occurs THEN DaughterCellKaryotype -> MAY_CHANGE

# CYTOKINESIS / ORIENTATION / ASYMMETRY
Cytokinesis -> partitions -> CYTOPLASM + CELLULAR_COMPONENTS -> between -> DAUGHTER_CELLS
CYTOKINESIS_FLOW := DIVISION_SITE_SELECTION -> CYTOKINETIC_MACHINERY_ASSEMBLY -> MEMBRANE_AND_CORTICAL_REMODELLING -> CONSTRICTION_OR_PARTITION_FORMATION -> FINAL_SEPARATION
Cytokinesis -> coordinated_with -> CHROMOSOME_SEGREGATION
ContractileRing -> actomyosin_structure_that -> DRIVES_CONSTRICTION_AS_APPLICABLE
CleavageFurrow -> forms_at -> DIVISION_PLANE_AS_APPLICABLE
CellPlate -> forms_during -> PLANT_CELL_CYTOKINESIS_AS_APPLICABLE
CellPlateFormation -> involves -> VESICLE_DELIVERY + MEMBRANE_FUSION + CELL_WALL_COMPONENT_DEPOSITION

DivisionPlane -> determines -> SPATIAL_PARTITION_OF_PARENT_CELL
DivisionOrientation -> influenced_by -> CELL_POLARITY + CELL_GEOMETRY + SPINDLE_ORIENTATION + TISSUE_CONTEXT
DivisionOrientation -> influences -> DAUGHTER_CELL_POSITION + TISSUE_ARCHITECTURE

AsymmetricCellDivision -> produces -> DAUGHTER_CELLS_WITH_DIFFERENT_STATES_OR_CONTENTS
AsymmetrySource := CELL_POLARITY | UNEQUAL_FATE_DETERMINANT_DISTRIBUTION | SPINDLE_ORIENTATION | DIFFERENTIAL_SIGNALING | UNEQUAL_SIZE_AS_APPLICABLE
AsymmetricDivision -> contributes_to -> DEVELOPMENT + CELL_FATE_DIVERSIFICATION

# DAUGHTER CELLS / ERRORS
DaughterCell -> produced_by -> CellDivision
DaughterCellState -> depends_on -> GENOME_CONTENT + CYTOPLASMIC_CONTENT + ORGANELLE_INHERITANCE + CELL_SIZE + FATE_DETERMINANTS + POST_DIVISION_SIGNALING
CellDivision -> must_coordinate -> CHROMOSOME_INHERITANCE + ORGANELLE_DISTRIBUTION + MEMBRANE_PARTITIONING

DIVISION_ERROR := REPLICATION_INCOMPLETION | CHROMOSOME_MISSEGREGATION | SPINDLE_DEFECT | CHECKPOINT_FAILURE | CYTOKINESIS_FAILURE | ABNORMAL_DIVISION_ORIENTATION
Aneuploidy -> may_result_from -> CHROMOSOME_MISSEGREGATION
CytokinesisFailure -> may_produce -> MULTINUCLEATE_OR_POLYPLOID_CELL_AS_APPLICABLE
DivisionError -> may_trigger -> CELL_CYCLE_ARREST + DNA_DAMAGE_RESPONSE + CELL_DEATH + OTHER_QUALITY_CONTROL_RESPONSE
DivisionQualityControl -> monitors -> DNA_INTEGRITY + REPLICATION_COMPLETION + SPINDLE_STATE + CHROMOSOME_ATTACHMENT + CYTOKINESIS
QualityControlFailure -> may_increase -> GENOME_INSTABILITY_RISK

# EVIDENCE / UNCERTAINTY / PROVENANCE
CellDivisionClaim -> supported_by -> Evidence
EVIDENCE_TYPE := LIVE_CELL_IMAGING | MICROSCOPIC | SUPER_RESOLUTION | ELECTRON_MICROSCOPIC | MOLECULAR | GENETIC | BIOCHEMICAL | CHROMOSOME_ANALYSIS | PERTURBATION | FUNCTIONAL | COMPUTATIONAL
Evidence -> has -> SOURCE + METHOD + CELL_OR_SAMPLE + DIVISION_TYPE + CELL_CYCLE_STAGE + CONDITION + QUALITY + UNCERTAINTY
CELL_DIVISION_UNCERTAINTY := MEASUREMENT_UNCERTAINTY + STAGE_CLASSIFICATION_UNCERTAINTY + ATTACHMENT_STATE_UNCERTAINTY + SEGREGATION_STATE_UNCERTAINTY + CELL_TO_CELL_VARIABILITY + MODEL_UNCERTAINTY
Uncertainty -> qualifies -> CellDivisionClaim + DivisionStage + ChromosomeState + SpindleState + DaughterCellOutcome
Provenance -> records -> CELL_IDENTITY + DIVISION_TYPE + CELL_CYCLE_STAGE + CHROMOSOME_STATE + SPINDLE_STATE + CYTOKINESIS_STATE + METHOD + CONDITION + OBSERVATION + TIME + VERSION
CellDivision -> linked_to -> Provenance

# REASONING
CELL_DIVISION_REASONING := IDENTIFY_DIVISION_EVENT -> CLASSIFY_DIVISION_TYPE -> MAP_CELL_CYCLE_STAGE -> MAP_DIVISION_COMMITMENT -> MAP_REPLICATION_COMPLETION -> MAP_CHROMOSOME_CONDENSATION -> MAP_SPINDLE_ASSEMBLY -> MAP_KINETOCHORE_ATTACHMENTS -> MAP_CHECKPOINT_STATE -> MAP_CHROMOSOME_ALIGNMENT -> MAP_CHROMATID_OR_HOMOLOG_SEPARATION -> MAP_CHROMOSOME_SEGREGATION -> MAP_CYTOKINESIS -> MAP_DIVISION_PLANE_AND_ORIENTATION -> MAP_ASYMMETRIC_PARTITIONING_AS_APPLICABLE -> MAP_DAUGHTER_CELL_OUTCOMES -> MAP_DIVISION_ERRORS -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF DNAReplication incomplete THEN DivisionProgression -> MAY_DELAY
IF SpindleBipolarity fails THEN ChromosomeSegregation -> MAY_BE_IMPAIRED
IF KinetochoreAttachment incorrect THEN SpindleCheckpoint -> MAY_REMAIN_ACTIVE
IF CheckpointFailure occurs THEN MissegregationRisk -> MAY_INCREASE
IF CohesionRelease occurs_at_correct_time THEN SisterChromatidSeparation -> MAY_PROCEED
IF Cytokinesis fails THEN DaughterCellSeparation -> MAY_FAIL
IF DivisionOrientation changes THEN DaughterCellPositionOrFateContext -> MAY_CHANGE
IF Evidence insufficient THEN CellDivisionClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION produces(CellDivision, DaughterCell)
RELATION coordinates(CellCycle, CellDivision)
RELATION duplicates(DNAReplication, GeneticMaterial)
RELATION compacts(ChromosomeCondensation, Chromatin)
RELATION subtype_of(Mitosis, CellDivision)
RELATION subtype_of(Meiosis, CellDivision)
RELATION organises(MitoticSpindle, ChromosomeSegregation)
RELATION binds(Kinetochore, SpindleMicrotubule)
RELATION monitors(SpindleAssemblyCheckpoint, KinetochoreAttachment)
RELATION maintains(Cohesin, SisterChromatidCohesion)
RELATION promotes(Separase, CohesionRelease)
RELATION distributes(ChromosomeSegregation, GeneticMaterial)
RELATION partitions(Cytokinesis, Cytoplasm)
RELATION drives(ContractileRing, Cytokinesis)
RELATION determines(DivisionPlane, CellularPartition)
RELATION produces(AsymmetricCellDivision, DaughterCell)
RELATION supports(Evidence, CellDivisionClaim)
RELATION records(Provenance, CellDivision)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "cell division" ~= "biological process producing daughter cells from a parent cell"
  "mitosis" ~= "eukaryotic nuclear division segregating duplicated chromosomes"
  "meiosis" ~= "specialised chromosome-reduction division associated with sexual reproduction"
  "mitotic spindle" ~= "microtubule apparatus that organises chromosome segregation"
  "kinetochore" ~= "chromosome-associated interface for spindle microtubule attachment"
  "spindle assembly checkpoint" ~= "surveillance system linking chromosome attachment state to anaphase onset"
  "chromosome segregation" ~= "distribution of chromosomes to daughter-cell destinations"
  "cytokinesis" ~= "physical partitioning of a parent cell into daughter cells"
  "asymmetric cell division" ~= "division producing daughter cells with unequal states contents or fates"
  "division plane" ~= "spatial plane defining cellular partition during cytokinesis"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  cell_cycle_mapping: 0.99
  replication_coordination_mapping: 0.99
  mitosis_meiosis_mapping: 0.99
  spindle_kinetochore_mapping: 0.99
  checkpoint_mapping: 0.99
  chromosome_segmentation_mapping: 0.99
  cytokinesis_mapping: 0.99
  asymmetric_division_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_division_observation:
    MAP division_type
    MAP cell_cycle_stage
    MAP chromosome_state
    MAP spindle_state
    MAP cytokinesis_state
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON chromosome_attachment_change:
    UPDATE kinetochore_state
    UPDATE checkpoint_state
    UPDATE segregation_risk
    PRESERVE provenance
  ON cytokinesis_event:
    UPDATE division_plane
    UPDATE contractile_or_cell_plate_state
    UPDATE daughter_cell_separation
    PRESERVE provenance
  ON division_error:
    UPDATE error_type
    UPDATE genome_stability_state
    UPDATE quality_control_response
    UPDATE uncertainty
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_CELL_DIVISION_ONTOLOGY
  reasoning_mode: CELL_DIVISION_CHROMOSOME_PARTITION_RELATIONAL
  preserve: [typed_entities, division_identity, division_type, cell_cycle_stage, replication_state, chromosome_state, spindle_state, kinetochore_state, checkpoint_state, segregation_state, cytokinesis_state, division_orientation, asymmetry_state, daughter_cell_state, division_errors, evidence, uncertainty, confidence, provenance]
  infer: [replication_division_dependencies, spindle_attachment_dependencies, checkpoint_response, chromosome_segmentation_state, cytokinesis_progress, division_orientation_effects, daughter_cell_outcomes, division_error_risk, evidence_strength]
  prohibit: [invented_division_observations, fabricated_chromosome_state, assumed_checkpoint_satisfaction_without_evidence, unsupported_daughter_cell_outcome, unsupported_causal_claims, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + CELL_CYCLE_REPLICATION + MITOSIS_MEIOSIS + SPINDLE_KINETOCHORE + CHECKPOINT_SEGREGATION + CYTOKINESIS_ORIENTATION_ASYMMETRY + DAUGHTER_CELLS_ERRORS + EVIDENCE_UNCERTAINTY_PROVENANCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW