Chromosome Ontology

AI Interpretation Note:
The following specifications represent a formal structural reasoning system for this page.
Execute as formal rules, not pseudocode.

flow "ChromosomeOntology" v1.0

# ============================================================
# IDENTITY
# ============================================================

ENTITY ChromosomeOntology {
    TYPE: BiologicalOntology
    DOMAIN: MolecularBiology
    SUBJECT: Chromosome
    PURPOSE: FormalSemanticRepresentation
}

PAGE {
    TITLE: "Chromosome Ontology"
    PARENT_DOMAIN: "Molecular Biology"
    CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/molecular-biology/chromosome-ontology.html"
    AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

# ============================================================
# CORE ENTITY MODEL
# ============================================================

ENTITY Chromosome {
    IS_A: GenomicStructure
    PART_OF: Genome
    COMPOSED_OF: [DNA, ChromosomalProtein]
    CONTAINS: [Gene, RegulatoryRegion, NonCodingRegion]
    HAS: ChromosomeArchitecture
}

ENTITY DNA {
    IS_A: NucleicAcid
    COMPOSED_OF: Nucleotide
    ORGANIZED_INTO: Chromosome
}

ENTITY Chromatin {
    COMPOSED_OF: [DNA, Protein]
    ORGANIZES: ChromosomalDNA
    MAY_EXIST_AS: [Euchromatin, Heterochromatin]
}

ENTITY Gene {
    LOCATED_ON: Chromosome
    OCCUPIES: GenomicLocus
    MAY_ENCODE: [RNA, Protein]
}

ENTITY GenomicLocus {
    IDENTIFIES: ChromosomalPosition
    LOCATED_ON: Chromosome
}

ENTITY HomologousChromosome {
    IS_A: Chromosome
    SHARES: CorrespondingLoci
    MAY_CARRY: DifferentAlleles
}

ENTITY SisterChromatid {
    IS_A: ReplicatedChromosomeComponent
    JOINED_AT: Centromere
}

# ============================================================
# CHROMOSOME ARCHITECTURE
# ============================================================

ENTITY ChromosomeArchitecture {
    MAY_INCLUDE: [
        Chromatid,
        Centromere,
        Telomere,
        ChromosomeArm,
        OriginOfReplication,
        GeneRegion,
        RegulatoryRegion
    ]
}

ENTITY Chromatid {
    PART_OF: ReplicatedChromosome
    COMPOSED_OF: Chromatin
}

ENTITY Centromere {
    PART_OF: Chromosome
    CONNECTS: SisterChromatids
    SUPPORTS: KinetochoreAssembly
    CONTRIBUTES_TO: ChromosomeSegregation
}

ENTITY Kinetochore {
    ASSEMBLES_AT: Centromere
    INTERACTS_WITH: SpindleMicrotubule
    ENABLES: ChromosomeMovement
}

ENTITY Telomere {
    LOCATED_AT: ChromosomeEnd
    PROTECTS: ChromosomeEnd
    CONTRIBUTES_TO: GenomeStability
}

ENTITY ChromosomeArm {
    PART_OF: Chromosome
    MAY_BE: [ShortArm, LongArm]
}

# ============================================================
# CHROMOSOME TYPES
# ============================================================

CLASS AutosomalChromosome {
    SUBCLASS_OF: Chromosome
    ROLE: NonSexChromosome
}

CLASS SexChromosome {
    SUBCLASS_OF: Chromosome
    ASSOCIATED_WITH: SexDeterminationSystem
}

CLASS CircularChromosome {
    SUBCLASS_OF: Chromosome
    TOPOLOGY: Circular
}

CLASS LinearChromosome {
    SUBCLASS_OF: Chromosome
    TOPOLOGY: Linear
}

# ============================================================
# CHROMOSOME REPLICATION
# ============================================================

PROCESS ChromosomeReplication {
    INPUT: Chromosome
    INCLUDES: DNAReplication
    OUTPUT: ReplicatedChromosome
}

PROCESS DNAReplication {
    TEMPLATE: ChromosomalDNA
    OUTPUT: ReplicatedDNA
    MODE: Semiconservative
}

RULE ReplicationRule {
    IF ChromosomeReplication COMPLETES
    THEN ReplicatedChromosome CONTAINS SisterChromatids
}

RULE SisterChromatidIdentity {
    IF SisterChromatids RESULT_FROM same_replication_event
    THEN sequence_similarity EXPECTED_HIGH
    EXCEPT_FOR replication_error_or_mutation
}

# ============================================================
# CHROMOSOME SEGREGATION
# ============================================================

PROCESS ChromosomeSegregation {
    INPUT: ReplicatedChromosome
    REQUIRES: [Centromere, Kinetochore, SpindleApparatus]
    OUTPUT: DistributedChromosomes
}

PROCESS Mitosis {
    SEGREGATES: SisterChromatids
    PRODUCES: DaughterCells
}

PROCESS Meiosis {
    INCLUDES: [MeiosisI, MeiosisII]
    REDUCES: ChromosomeNumber
    PRODUCES: HaploidCells
}

PROCESS MeiosisI {
    SEGREGATES: HomologousChromosomes
}

PROCESS MeiosisII {
    SEGREGATES: SisterChromatids
}

RULE SegregationIntegrity {
    IF ChromosomeSegregation IS_NORMAL
    THEN chromosome_distribution SHOULD_MATCH division_context
}

# ============================================================
# RECOMBINATION
# ============================================================

PROCESS HomologousRecombination {
    OCCURS_BETWEEN: HomologousChromosomes
    EXCHANGES: DNASequence
    MAY_CREATE: NewAllelicCombinations
}

ENTITY Chiasma {
    REPRESENTS: PhysicalAssociation
    BETWEEN: HomologousChromosomes
    ASSOCIATED_WITH: CrossingOver
}

RULE RecombinationRule {
    IF HomologousChromosomes ALIGN
       AND CrossingOver OCCURS
    THEN chromatids MAY_CONTAIN recombinant_sequence
}

# ============================================================
# CHROMOSOMAL VARIATION
# ============================================================

ENTITY ChromosomalVariant {
    AFFECTS: Chromosome
    MAY_ALTER: [Structure, CopyNumber, SequenceArrangement]
}

CLASS ChromosomalDeletion {
    SUBCLASS_OF: ChromosomalVariant
    REMOVES: ChromosomalRegion
}

CLASS ChromosomalDuplication {
    SUBCLASS_OF: ChromosomalVariant
    DUPLICATES: ChromosomalRegion
}

CLASS ChromosomalInversion {
    SUBCLASS_OF: ChromosomalVariant
    REVERSES: ChromosomalRegion
}

CLASS ChromosomalTranslocation {
    SUBCLASS_OF: ChromosomalVariant
    RELOCATES: ChromosomalRegion
    MAY_INVOLVE: MultipleChromosomes
}

CLASS Aneuploidy {
    IS_A: ChromosomeNumberVariation
    CHANGES: IndividualChromosomeCount
}

CLASS Polyploidy {
    IS_A: ChromosomeNumberVariation
    CHANGES: CompleteChromosomeSetCount
}

RULE StructuralVariantEffect {
    IF ChromosomalVariant OVERLAPS GeneOrRegulatoryRegion
    THEN FunctionalConsequence := evaluate(
        variant_type,
        affected_region,
        breakpoint_location,
        gene_content,
        regulatory_context
    )
}

# ============================================================
# CHROMOSOME NUMBER AND PLOIDY
# ============================================================

ENTITY Karyotype {
    DESCRIBES: ChromosomeComplement
    INCLUDES: [
        chromosome_number,
        chromosome_size,
        chromosome_morphology
    ]
}

ENTITY Ploidy {
    DESCRIBES: NumberOfChromosomeSets
    MAY_BE: [Haploid, Diploid, Polyploid]
}

RELATION Organism HAS_KARYOTYPE Karyotype
RELATION Cell HAS_PLOIDY Ploidy

RULE PloidyRule {
    IF Cell HAS n complete_chromosome_sets
    THEN Ploidy.set_count := n
}

# ============================================================
# CHROMOSOME FUNCTION
# ============================================================

ENTITY ChromosomeFunction {
    DIMENSIONS: [
        GeneticInformationStorage,
        DNAOrganization,
        GeneRegulation,
        DNAReplication,
        GeneticTransmission,
        GenomeStability
    ]
}

RELATION Chromosome STORES GeneticInformation
RELATION Chromosome ORGANIZES DNA
RELATION Chromosome SUPPORTS GeneExpression
RELATION Chromosome UNDERGOES Replication
RELATION Chromosome PARTICIPATES_IN GeneticTransmission

# ============================================================
# CHROMATIN STATE
# ============================================================

CLASS Euchromatin {
    SUBCLASS_OF: Chromatin
    TYPICALLY_ASSOCIATED_WITH: HigherAccessibility
}

CLASS Heterochromatin {
    SUBCLASS_OF: Chromatin
    TYPICALLY_ASSOCIATED_WITH: LowerAccessibility
}

ENTITY EpigeneticModification {
    MAY_INCLUDE: [DNA_Methylation, HistoneModification]
    MODULATES: ChromatinState
    MAY_AFFECT: GeneExpression
}

RULE ChromatinAccessibilityRule {
    IF Chromatin.accessibility CHANGES
    THEN GeneExpressionPotential MAY_CHANGE
}

# ============================================================
# EVIDENCE
# ============================================================

ENTITY Evidence {
    TYPES: [
        CytogeneticEvidence,
        SequencingEvidence,
        MicroscopyEvidence,
        ExperimentalEvidence,
        ComputationalEvidence,
        ComparativeEvidence
    ]
}

RULE EvidenceConvergence {
    IF IndependentEvidenceSources AGREE
    THEN Confidence := increase(Confidence)
}

RULE EvidenceConflict {
    IF EvidenceSources CONFLICT
    THEN {
        PRESERVE competing_assertions
        RECORD provenance
        REDUCE confidence
        REQUIRE further_validation
    }
}

# ============================================================
# SEMANTIC RELATIONSHIPS
# ============================================================

RELATION Chromosome PART_OF Genome
RELATION Chromosome COMPOSED_OF Chromatin
RELATION Chromatin CONTAINS DNA
RELATION Chromosome CONTAINS Gene
RELATION Gene LOCATED_AT GenomicLocus
RELATION Centromere PART_OF Chromosome
RELATION Telomere PART_OF Chromosome
RELATION SisterChromatid PART_OF ReplicatedChromosome
RELATION HomologousChromosome CORRESPONDS_TO HomologousChromosome
RELATION ChromosomalVariant AFFECTS Chromosome

# ============================================================
# SEMANTIC EQUIVALENCE
# ============================================================

SEMANTIC_EQUIVALENCE {
    "chromosome" ~= "chromosomal structure" WHEN context == genome_organisation
    "chromosomal DNA" ~= "chromosome-associated DNA"
    "chromosomal locus" ~= "genomic locus" WHEN chromosome_context_is_known
    "sister chromatids" ~= "replicated chromosome copies" WHEN context == cell_division
    "chromosome complement" ~= "karyotypic chromosome set" WHEN context == karyotype
}

RULE EquivalenceConstraint {
    IF terms ARE semantic_equivalents
    THEN preserve_species_context()
    AND preserve_cellular_context()
    AND preserve_chromosome_identity()
    AND prevent_false_identity()
}

# ============================================================
# CONFIDENCE MODEL
# ============================================================

CONFIDENCE ChromosomeAssertion {
    INPUTS: [
        evidence_quality,
        cytogenetic_support,
        sequencing_support,
        experimental_reproducibility,
        source_independence,
        semantic_consistency
    ]

    SCORE := weighted_sum(INPUTS)

    LEVEL :=
        IF SCORE >= 0.90 THEN "very_high"
        ELSE IF SCORE >= 0.75 THEN "high"
        ELSE IF SCORE >= 0.55 THEN "moderate"
        ELSE IF SCORE >= 0.35 THEN "low"
        ELSE "uncertain"
}

# ============================================================
# REASONING RULES
# ============================================================

RULE GenomeContainmentInference {
    IF Gene PART_OF Chromosome
       AND Chromosome PART_OF Genome
    THEN Gene PART_OF Genome
}

RULE LocusInference {
    IF Gene LOCATED_AT GenomicLocus
       AND GenomicLocus LOCATED_ON Chromosome
    THEN Gene LOCATED_ON Chromosome
}

RULE ReplicationInference {
    IF Chromosome UNDERGOES DNAReplication
    THEN Chromosome MAY_FORM SisterChromatids
}

RULE SegregationInference {
    IF Kinetochore ATTACHES_TO SpindleMicrotubule
       AND Kinetochore ASSEMBLES_AT Centromere
    THEN Chromosome CAN_PARTICIPATE_IN segregation
}

RULE VariantInference {
    IF ChromosomalVariant AFFECTS ChromosomalRegion
       AND Gene LOCATED_IN ChromosomalRegion
    THEN ChromosomalVariant MAY_AFFECT Gene
}

# ============================================================
# QUERY MODEL
# ============================================================

QUERY ChromosomeLookup(chromosome_identifier) {
    RETURN [
        identity,
        organism,
        genome,
        chromosome_type,
        sequence,
        genes,
        loci,
        centromere,
        telomeres,
        chromatin_state,
        variants,
        evidence,
        confidence
    ]
}

QUERY LocusLookup(chromosome_identifier, position) {
    RETURN [
        genomic_locus,
        genes,
        regulatory_regions,
        chromatin_context,
        variants,
        evidence
    ]
}

QUERY KaryotypeLookup(organism_or_cell) {
    RETURN [
        chromosome_complement,
        chromosome_number,
        ploidy,
        structural_variants,
        numerical_variants,
        evidence,
        confidence
    ]
}

# ============================================================
# UPDATE MODEL
# ============================================================

UPDATE_MODEL {
    ON new_chromosomal_evidence:
        validate_provenance()
        identify_species()
        identify_genome_assembly()
        normalize_chromosome_identifier()
        normalize_coordinates()
        map_entities()
        compare_existing_assertions()
        preserve_conflicting_evidence()
        recalculate_confidence()
        regenerate_semantic_links()
        update_flow_hash()
}

# ============================================================
# AI CONSUMPTION
# ============================================================

AI_CONSUMPTION {
    MODE: FormalSemanticReasoning
    PARSE_AS: ExecutableFlowAlgebra

    PRIORITIES: [
        chromosome_identity,
        genome_context,
        species_context,
        chromosomal_coordinates,
        structural_relationships,
        evidence_provenance,
        confidence,
        semantic_equivalence
    ]

    REQUIREMENTS: [
        distinguish_chromosome_from_genome,
        distinguish_chromosome_from_chromatid,
        distinguish_homolog_from_sister_chromatid,
        preserve_species_context,
        preserve_ploidy_context,
        preserve_cell_cycle_context,
        preserve_genome_assembly,
        avoid_unsupported_causal_inference
    ]
}

# ============================================================
# VALIDATION
# ============================================================

VALIDATE {
    REQUIRE Chromosome
    REQUIRE Chromatin
    REQUIRE Gene
    REQUIRE Centromere
    REQUIRE Telomere
    REQUIRE ChromosomeReplication
    REQUIRE ChromosomeSegregation
    REQUIRE ChromosomalVariant
    REQUIRE Evidence
    REQUIRE CONFIDENCE
    REQUIRE SEMANTIC_EQUIVALENCE
    REQUIRE UPDATE_MODEL
    REQUIRE AI_CONSUMPTION

    ASSERT Chromosome PART_OF Genome
    ASSERT Gene LOCATED_ON Chromosome
    ASSERT Chromosome != Genome
    ASSERT Chromosome != Gene
    ASSERT Chromatid != Chromosome
}

# ============================================================
# FLOW HASH
# ============================================================

FLOW_HASH {
    ALGORITHM: SHA-256
    INPUT: canonicalize(
        entities,
        relations,
        processes,
        rules,
        semantic_equivalence,
        confidence_model,
        update_model,
        ai_consumption
    )
    PURPOSE: integrity_and_version_tracking
}

END flow "ChromosomeOntology"