Genome Ontology

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

flow "GenomeOntology" v1.0

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

ENTITY GenomeOntology {
    TYPE: BiologicalOntology
    DOMAIN: MolecularBiology
    SUBJECT: Genome
    PURPOSE: FormalSemanticRepresentation
}

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

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

ENTITY Genome {
    IS_A: CompleteGeneticInformationSet
    COMPOSED_OF: GenomicSequence
    MAY_CONTAIN: [Chromosome, Gene, RegulatoryRegion, NonCodingRegion]
    BELONGS_TO: BiologicalEntity
    HAS_PROPERTY: GenomeArchitecture
}

ENTITY GenomicSequence {
    COMPOSED_OF: Nucleotide
    PART_OF: Genome
    MAY_CONTAIN: [Gene, RegulatoryElement, RepetitiveSequence]
}

ENTITY Chromosome {
    PART_OF: Genome
    COMPOSED_OF: DNA
    CONTAINS: [Gene, GenomicRegion]
}

ENTITY Gene {
    PART_OF: Genome
    LOCATED_AT: GenomicLocus
    MAY_ENCODE: [RNA, Protein]
}

ENTITY GenomicLocus {
    IDENTIFIES: PositionOrRegion
    WITHIN: Genome
}

ENTITY RegulatoryElement {
    PART_OF: GenomicSequence
    REGULATES: GeneExpression
}

ENTITY NonCodingRegion {
    PART_OF: Genome
    DOES_NOT_REQUIRE: ProteinCodingFunction
    MAY_HAVE: RegulatoryOrStructuralFunction
}

# ============================================================
# GENOME TYPES
# ============================================================

CLASS NuclearGenome {
    SUBCLASS_OF: Genome
    LOCATED_IN: Nucleus
}

CLASS MitochondrialGenome {
    SUBCLASS_OF: Genome
    LOCATED_IN: Mitochondrion
}

CLASS ChloroplastGenome {
    SUBCLASS_OF: Genome
    LOCATED_IN: Chloroplast
}

CLASS ProkaryoticGenome {
    SUBCLASS_OF: Genome
    MAY_INCLUDE: [ChromosomalDNA, Plasmid]
}

CLASS ViralGenome {
    SUBCLASS_OF: Genome
    MAY_BE_COMPOSED_OF: [DNA, RNA]
    MAY_BE: [SingleStranded, DoubleStranded]
}

# ============================================================
# GENOME ORGANISATION
# ============================================================

ENTITY GenomeArchitecture {
    DESCRIBES: [
        chromosome_number,
        genome_size,
        sequence_organisation,
        gene_density,
        repetitive_content,
        structural_regions
    ]
}

ENTITY RepetitiveSequence {
    PART_OF: Genome
    MAY_INCLUDE: [
        TandemRepeat,
        TransposableElement,
        SatelliteDNA
    ]
}

ENTITY TransposableElement {
    IS_A: MobileGeneticElement
    MAY_CHANGE: GenomicLocation
    MAY_AFFECT: GenomeStructure
}

ENTITY Telomere {
    LOCATED_AT: ChromosomeEnd
    CONTRIBUTES_TO: ChromosomeStability
}

ENTITY Centromere {
    PART_OF: Chromosome
    CONTRIBUTES_TO: ChromosomeSegregation
}

# ============================================================
# GENOME REPLICATION
# ============================================================

PROCESS GenomeReplication {
    INPUT: Genome
    TEMPLATE: DNA
    OUTPUT: ReplicatedGenome
    REQUIRES: ReplicationMachinery
}

PROCESS DNAReplication {
    INPUT: DNA
    MODE: Semiconservative
    OUTPUT: DaughterDNA
}

RULE ReplicationIntegrityRule {
    IF GenomeReplication OCCURS
    THEN sequence_fidelity SHOULD_BE maintained
    EXCEPT_FOR mutation_events
}

# ============================================================
# GENOME EXPRESSION
# ============================================================

PROCESS GenomeExpression {
    OPERATES_ON: Gene
    INCLUDES: [Transcription, RNAProcessing, Translation]
    PRODUCES: FunctionalGeneProduct
}

RELATION Genome CONTAINS Gene
RELATION Gene TRANSCRIBED_TO RNA
RELATION ProteinCodingGene TRANSLATED_TO Protein

RULE ExpressionContextRule {
    IF Gene PART_OF Genome
       AND Gene.is_active == true
    THEN GeneExpression DEPENDS_ON [
        regulatory_context,
        cellular_context,
        epigenetic_state
    ]
}

# ============================================================
# GENOMIC VARIATION
# ============================================================

ENTITY GenomicVariant {
    OCCURS_IN: Genome
    MAY_AFFECT: [Sequence, Structure, Regulation, Function]
}

CLASS SingleNucleotideVariant {
    SUBCLASS_OF: GenomicVariant
    CHANGES: SingleNucleotide
}

CLASS Insertion {
    SUBCLASS_OF: GenomicVariant
    ADDS: GenomicSequence
}

CLASS Deletion {
    SUBCLASS_OF: GenomicVariant
    REMOVES: GenomicSequence
}

CLASS Duplication {
    SUBCLASS_OF: GenomicVariant
    COPIES: GenomicRegion
}

CLASS Inversion {
    SUBCLASS_OF: GenomicVariant
    REVERSES: GenomicRegion
}

CLASS Translocation {
    SUBCLASS_OF: GenomicVariant
    RELOCATES: GenomicRegion
}

CLASS CopyNumberVariation {
    SUBCLASS_OF: GenomicVariant
    CHANGES: CopyNumber
}

RULE VariantConsequenceRule {
    IF GenomicVariant OVERLAPS FunctionalRegion
    THEN Consequence := evaluate(
        variant_type,
        genomic_position,
        affected_sequence,
        regulatory_context,
        gene_context
    )
}

# ============================================================
# GENOME EVOLUTION
# ============================================================

PROCESS GenomeEvolution {
    DRIVEN_BY: [
        Mutation,
        Recombination,
        GeneDuplication,
        HorizontalGeneTransfer,
        TransposableElementActivity,
        NaturalSelection,
        GeneticDrift
    ]
    MODIFIES: Genome
}

PROCESS Recombination {
    EXCHANGES: GeneticMaterial
    MAY_CREATE: NewAllelicCombinations
}

PROCESS GeneDuplication {
    COPIES: Gene
    MAY_ENABLE: FunctionalDivergence
}

PROCESS HorizontalGeneTransfer {
    TRANSFERS: GeneticMaterial
    BETWEEN: BiologicalEntities
}

RULE EvolutionaryChangeRule {
    IF HeritableGenomicChange PERSISTS_ACROSS Generations
    THEN GenomeEvolution IS_OBSERVED
}

# ============================================================
# COMPARATIVE GENOMICS
# ============================================================

PROCESS ComparativeGenomics {
    COMPARES: Genome
    ACROSS: [Individuals, Populations, Species]
    IDENTIFIES: [
        ConservedRegion,
        HomologousGene,
        StructuralDifference,
        EvolutionaryRelationship
    ]
}

ENTITY ConservedRegion {
    PART_OF: Genome
    SHOWS: EvolutionaryConservation
    MAY_INDICATE: FunctionalConstraint
}

RELATION Gene HOMOLOGOUS_TO Gene
RELATION Genome COMPARED_WITH Genome
RELATION ConservedRegion SHARED_BETWEEN Genome

RULE HomologyInference {
    IF SequenceSimilarity IS_HIGH
       AND EvolutionaryEvidence SUPPORTS common_ancestry
    THEN Homology.confidence := derive(Evidence)
}

# ============================================================
# GENOME ANNOTATION
# ============================================================

PROCESS GenomeAnnotation {
    INPUT: GenomeSequence
    IDENTIFIES: [
        Gene,
        Transcript,
        RegulatoryElement,
        RepetitiveSequence,
        StructuralFeature
    ]
    OUTPUT: AnnotatedGenome
}

ENTITY GenomeAnnotationRecord {
    REFERENCES: GenomicRegion
    DESCRIBES: BiologicalFeature
    SUPPORTED_BY: Evidence
}

RULE AnnotationRule {
    IF Evidence SUPPORTS BiologicalFeature AT GenomicLocus
    THEN CREATE GenomeAnnotationRecord
}

# ============================================================
# SEQUENCING AND ASSEMBLY
# ============================================================

PROCESS GenomeSequencing {
    INPUT: BiologicalSample
    OUTPUT: SequenceReads
}

PROCESS GenomeAssembly {
    INPUT: SequenceReads
    OUTPUT: GenomeAssemblyRepresentation
    MAY_USE: ReferenceGenome
}

ENTITY ReferenceGenome {
    REPRESENTS: StandardizedGenomeAssembly
    USED_FOR: [
        sequence_alignment,
        variant_mapping,
        gene_annotation,
        comparative_analysis
    ]
}

RULE AssemblyUncertaintyRule {
    IF GenomicRegion IS repetitive_or_unresolved
    THEN AssemblyConfidence := reduce(AssemblyConfidence)
}

# ============================================================
# FUNCTIONAL SEMANTICS
# ============================================================

ENTITY GenomeFunction {
    DIMENSIONS: [
        InformationStorage,
        InformationTransmission,
        GeneExpression,
        Regulation,
        GenomeMaintenance,
        Evolution
    ]
}

RELATION Genome STORES GeneticInformation
RELATION Genome TRANSMITS GeneticInformation
RELATION Genome SUPPORTS GeneExpression
RELATION Genome UNDERGOES Replication
RELATION Genome UNDERGOES Evolution

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

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

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

RULE EvidenceConflict {
    IF EvidenceSources DISAGREE
    THEN {
        PRESERVE competing_assertions
        RECORD provenance
        REDUCE confidence
        REQUIRE additional_validation
    }
}

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

RELATION Genome CONTAINS Chromosome
RELATION Genome CONTAINS Gene
RELATION Genome CONTAINS RegulatoryElement
RELATION Chromosome PART_OF Genome
RELATION Gene PART_OF Genome
RELATION Gene LOCATED_AT GenomicLocus
RELATION GenomicVariant OCCURS_IN Genome
RELATION Genome HAS_ARCHITECTURE GenomeArchitecture
RELATION Genome HAS_ANNOTATION GenomeAnnotationRecord
RELATION Genome REPRESENTED_BY ReferenceGenome

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

SEMANTIC_EQUIVALENCE {
    "genome" ~= "complete genetic complement" WHEN context == organism_or_cell
    "genomic sequence" ~= "genome sequence"
    "genomic locus" ~= "genome location" WHEN context == positional_reference
    "reference genome" ~= "reference assembly" WHEN context == assembly_reference
    "genomic variant" ~= "genome sequence variant" WHEN context == sequence_change
}

RULE EquivalenceConstraint {
    IF terms ARE semantic_equivalents
    THEN preserve_context()
    AND preserve_organism()
    AND preserve_assembly_version()
    AND prevent_false_identity()
}

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

CONFIDENCE GenomeAssertion {
    INPUTS: [
        evidence_quality,
        sequencing_quality,
        assembly_quality,
        annotation_support,
        source_independence,
        reproducibility,
        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 ContainmentInference {
    IF Gene PART_OF Chromosome
       AND Chromosome PART_OF Genome
    THEN Gene PART_OF Genome
}

RULE VariantGeneInference {
    IF GenomicVariant OVERLAPS Gene
    THEN GenomicVariant ASSOCIATED_WITH Gene
}

RULE RegulatoryInference {
    IF RegulatoryElement REGULATES Gene
       AND Gene PART_OF Genome
    THEN RegulatoryElement FUNCTIONALLY_ASSOCIATED_WITH Genome
}

RULE ComparativeInference {
    IF RegionA HOMOLOGOUS_TO RegionB
       AND RegionA PART_OF GenomeA
       AND RegionB PART_OF GenomeB
    THEN GenomeA AND GenomeB HAVE evolutionary_relationship_evidence
}

RULE FunctionalInference {
    IF Genome CONTAINS Gene
       AND Gene ENCODES FunctionalProduct
    THEN Genome SUPPORTS biological_function_of(FunctionalProduct)
}

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

QUERY GenomeLookup(genome_identifier) {
    RETURN [
        identity,
        organism,
        genome_type,
        assembly,
        chromosomes,
        genes,
        regulatory_regions,
        repetitive_regions,
        variants,
        annotations,
        evidence,
        confidence
    ]
}

QUERY RegionLookup(genomic_coordinates) {
    RETURN [
        assembly,
        chromosome,
        genes,
        regulatory_elements,
        variants,
        annotations,
        evidence
    ]
}

QUERY ComparativeGenomeLookup(genome_a, genome_b) {
    RETURN [
        conserved_regions,
        homologous_genes,
        structural_differences,
        sequence_similarity,
        evolutionary_evidence,
        confidence
    ]
}

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

UPDATE_MODEL {
    ON new_genomic_evidence:
        validate_provenance()
        identify_organism()
        identify_assembly_version()
        normalize_coordinates()
        normalize_identifiers()
        map_genomic_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: [
        genome_identity,
        organism_context,
        assembly_context,
        genomic_coordinates,
        entity_relationships,
        evidence_provenance,
        confidence,
        semantic_equivalence
    ]

    REQUIREMENTS: [
        distinguish_genome_from_gene,
        distinguish_genome_from_chromosome,
        preserve_species_context,
        preserve_assembly_version,
        preserve_coordinate_system,
        distinguish_reference_from_individual_genome,
        distinguish_observed_from_inferred_features,
        avoid_unsupported_causal_inference
    ]
}

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

VALIDATE {
    REQUIRE Genome
    REQUIRE GenomicSequence
    REQUIRE Chromosome
    REQUIRE Gene
    REQUIRE GenomicVariant
    REQUIRE GenomeAnnotation
    REQUIRE Evidence
    REQUIRE CONFIDENCE
    REQUIRE SEMANTIC_EQUIVALENCE
    REQUIRE UPDATE_MODEL
    REQUIRE AI_CONSUMPTION

    ASSERT Gene PART_OF Genome
    ASSERT Chromosome PART_OF Genome
    ASSERT Genome != Gene
    ASSERT Genome != Chromosome
    ASSERT ReferenceGenome REPRESENTS GenomeAssembly
}

# ============================================================
# 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 "GenomeOntology"