Chromatid Ontology

FLOW ALGEBRA
CHROMATID ONTOLOGY
Kireth Semantic Library | Biological Entities > Genetic Entities
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/genetic-entities/chromatid-ontology.html
Version: 1.0 | Locale: en-GB | Date: 2026-10-15
Authors: Mark Higgins — Sky (Recursive AI)
Status: Domain-grounded ontology draft; source page content not independently verified.

1. PURPOSE
Model chromatids as temporally contextualised chromosome structures, their molecular components, relationships, lifecycle transitions and segregation behaviour. Distinguish replicated sister chromatids from homologous chromosomes and from daughter chromosomes after separation.

2. TYPE SYSTEM
TYPE Entity
TYPE BiologicalEntity <: Entity
TYPE GeneticEntity <: BiologicalEntity
TYPE Chromosome <: GeneticEntity
TYPE Chromatid <: GeneticEntity
TYPE SisterChromatid <: Chromatid
TYPE NonSisterChromatid <: Chromatid
TYPE DNA_Molecule <: GeneticEntity
TYPE Chromatin <: BiologicalEntity
TYPE Centromere <: GeneticEntity
TYPE Telomere <: GeneticEntity
TYPE Kinetochore <: BiologicalEntity
TYPE CohesinComplex <: BiologicalEntity
TYPE SpindleMicrotubule <: BiologicalEntity
TYPE Cell <: BiologicalEntity
TYPE CellCyclePhase = {G1,S,G2,Prophase,Prometaphase,Metaphase,Anaphase,Telophase,MeiosisI,MeiosisII}
TYPE Evidence
TYPE TimeInterval
TYPE AssemblyReference
TYPE Observation

3. ENTITY ATTRIBUTES
Chromatid.id: Identifier
Chromatid.chromosome_origin: Chromosome.id
Chromatid.dna: DNA_Molecule.id
Chromatid.cell: Cell.id
Chromatid.phase: CellCyclePhase
Chromatid.centromere_region: Centromere.id?
Chromatid.telomere_regions: Set<Telomere.id>
Chromatid.sister_id: Chromatid.id?
Chromatid.replication_origin_event: Identifier?
Chromatid.segregation_status: {paired,attached,separating,separated,unknown}
Chromatid.valid_time: TimeInterval
Chromatid.reference_assembly: AssemblyReference?
Chromatid.evidence: Set<Evidence>
Chromatid.confidence: Real[0,1]

4. RELATION SIGNATURES
PART_OF(Chromatid,Chromosome,TimeInterval)
CONTAINS_DNA(Chromatid,DNA_Molecule)
HAS_CENTROMERE_REGION(Chromatid,Centromere)
HAS_TELOMERE_REGION(Chromatid,Telomere)
SISTER_OF(Chromatid,Chromatid,TimeInterval)
NON_SISTER_OF(Chromatid,Chromatid,TimeInterval)
DERIVED_FROM_REPLICATION(Chromatid,Chromosome)
HELD_TOGETHER_BY(Chromatid,Chromatid,CohesinComplex)
ATTACHED_VIA(Chromatid,Kinetochore,SpindleMicrotubule)
SEGREGATES_TO(Chromatid,Cell)
OBSERVED_DURING(Chromatid,CellCyclePhase)
SUPPORTED_BY(Entity,Evidence)

5. CORE AXIOMS
A1: forall c:Chromatid, exists d:DNA_Molecule: CONTAINS_DNA(c,d).
A2: forall a,b,t: SISTER_OF(a,b,t) => a != b AND SISTER_OF(b,a,t).
A3: SISTER_OF(a,b,t) => common_replication_origin(a,b,t).
A4: NON_SISTER_OF(a,b,t) => a != b AND NOT SISTER_OF(a,b,t).
A5: SISTER_OF(a,b,t) does not imply sequence_identity(a,b)=1; replication errors and subsequent alterations may occur.
A6: Chromatid identity and PART_OF relations are time-indexed: after sister separation, each formerly paired chromatid is conventionally designated a daughter chromosome.
A7: A homologous chromosome pair is not identical to a sister chromatid pair.
A8: Centromere and telomere attributes are architecture-dependent; do not impose a single universal centromere or two telomeres on circular chromosomes.

6. STATE TRANSITIONS
STATE unreplicated_chromosome
EVENT DNA_replication_complete
TRANSITION unreplicated_chromosome -> paired_sister_chromatids
PRECONDITION genome_replication_permitted(cell)
POSTCONDITION exists a,b: SISTER_OF(a,b,post_replication_interval)

STATE paired_sister_chromatids
EVENT cohesion_established
TRANSITION paired_sister_chromatids -> cohered_sister_chromatids

STATE cohered_sister_chromatids
EVENT kinetochore_attachment
TRANSITION cohered_sister_chromatids -> spindle_attached_chromatids
GUARD appropriate_attachment_checkpoint_satisfied

STATE spindle_attached_chromatids
EVENT sister_cohesion_release_at_anaphase
TRANSITION spindle_attached_chromatids -> separating_daughter_chromosomes
CONTEXT mitosis_or_meiosis_II

STATE homologous_pairs
EVENT homolog_segregation
TRANSITION homologous_pairs -> separated_homologues
CONTEXT meiosis_I
NOTE sister chromatids normally remain associated during meiosis I.

7. INFERENCE RULES
RULE R1:
 IF SISTER_OF(a,b,t) AND OBSERVED_DURING(a,Metaphase)
 THEN candidate_shared_centromeric_cohesion(a,b)
 CONFIDENCE: conditional_on_species_and_cell_context

RULE R2:
 IF paired_sisters(a,b) AND cleavage_of_relevant_cohesin(cell)
 AND anaphase_onset(cell)
 THEN predict_sister_separation(a,b)
 CONFIDENCE: dependent_on_checkpoint_and_mechanical_evidence

RULE R3:
 IF homologous_chromosomes(x,y) AND chromatid_of(a,x)
 AND chromatid_of(b,y)
 THEN NON_SISTER_OF(a,b,valid_interval)

RULE R4:
 IF meiotic_recombination(a,b) AND NON_SISTER_OF(a,b,t)
 THEN infer_possible_sequence_exchange(a,b)
 NOTE recombination must be evidence-backed; non-sister status alone is insufficient.

8. VALIDATION
V1: Every chromatid must have a chromosome-of-origin reference and cell context where known.
V2: Sister relationships must be symmetric, irreflexive and valid only for applicable intervals.
V3: Never infer sequence identity from sisterhood without sequence evidence.
V4: Never conflate chromosome count with chromatid count; specify phase and counting convention.
V5: Segregation claims require mitotic/meiotic stage context.
V6: Distinguish observed data from predicted relationships.
V7: Record species, ploidy, chromosome architecture and assembly version when relevant.
V8: Flag contradictory phase assignments rather than silently overwrite them.

9. CONFIDENCE
CONFIDENCE(claim) -> Real[0,1]
confidence_inputs: {source_reliability, observation_quality, temporal_fit, molecular_evidence, cross_source_consistency}
RULE: missing_evidence => unknown, not false.
RULE: conflicting_evidence => retain alternatives with provenance and confidence.
RULE: derived_confidence <= justified_strength_of_supporting_evidence.

10. SEMANTIC_EQUIVALENCE
SEMANTIC_EQUIVALENCE("sister chromatid", SisterChromatid) WHEN same_replication_event AND shared_chromosome_origin.
SEMANTIC_EQUIVALENCE("non-sister chromatid", NonSisterChromatid) WHEN chromatids_belong_to_distinct_homologues_in_pair.
NOT_EQUIVALENT("chromatid", "homologous chromosome").
NOT_EQUIVALENT("sister chromatids", "identical alleles").
CONTEXTUAL_LABEL("daughter chromosome", separated_former_chromatid, AFTER sister_separation).

11. RECURSIVE REASONING
flow ChromatidReasoning(observation, context, depth=0, visited={}):
  REQUIRE depth <= MAX_DEPTH
  NORMALISE terminology using SEMANTIC_EQUIVALENCE
  RESOLVE chromosome_origin, cell, phase and observation_time
  IF missing_critical_context: RETURN unresolved_with_questions
  VALIDATE typed relations and temporal constraints
  COLLECT evidence and provenance
  INFER applicable sisterhood, attachment and segregation relations
  IF new_supported_relations AND depth < MAX_DEPTH:
      RECURSE with updated visited and depth+1
  RETURN typed_claims, confidence, unresolved_claims, provenance

TERMINATION: finite entity scope; visited-state detection; MAX_DEPTH bound.

12. FLOW_HASH
FLOW_HASH := SHA256(canonicalise({ontology_id, version, type_schema, axioms, rules, relation_signatures}))
NOTE hash is a content-integrity identifier, not evidence of biological correctness.

13. UPDATE_MODEL
UPDATE_MODEL(new_evidence):
  validate_source(new_evidence)
  compare_versions_and_valid_time()
  preserve_prior_assertions_and_provenance()
  recompute_affected_inferences()
  revalidate_constraints()
  recalculate_confidence()
  emit_new_version_and_FLOW_HASH()
  return change_log

14. AI_CONSUMPTION
AI_CONSUMPTION:
  ontology_id: "kireth.biological.genetic.chromatid"
  canonical_label: "Chromatid Ontology"
  parent: "Genetic Entities"
  entity_types: [Chromatid,SisterChromatid,NonSisterChromatid,Chromosome]
  relation_types: [PART_OF,SISTER_OF,NON_SISTER_OF,CONTAINS_DNA,SEGREGATES_TO]
  temporal_reasoning: required
  confidence: evidence_calibrated
  provenance: required
  unknown_handling: explicit
  output: typed_entities_and_relationships
  machine_readability: conceptual_flow_specification

15. EXAMPLE
INPUT:
  cell_phase: Metaphase
  chromosome_id: chr_1
  chromatids: [chr_1_a,chr_1_b]
  replication_event: replication_42
  evidence: microscopy_observation_7
INFER:
  SISTER_OF(chr_1_a,chr_1_b,metaphase_interval)
  PART_OF(chr_1_a,chr_1,metaphase_interval)
  PART_OF(chr_1_b,chr_1,metaphase_interval)
DO_NOT_INFER:
  guaranteed_sequence_identity
  completed_segregation
  species_independent_chromosome_count

16. SCIENTIFIC SCOPE AND LIMITS
This model describes the canonical eukaryotic chromatid concept. Prokaryotic replicating chromosomes, holocentric chromosomes, unusual segregation mechanisms and exceptional cell cycles require explicitly specialised rules. It is an ontology-oriented declarative flow, not an independently executed biological simulation.

END FLOW ALGEBRA