Epigenetics Ontology

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

flow "EpigeneticsOntology" v1.0

ENTITY EpigeneticsOntology {
  TYPE: BiologicalOntology
  DOMAIN: MolecularBiology
  SUBJECT: Epigenetics
  PURPOSE: FormalSemanticRepresentation
}

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

ENTITY Epigenetics {
  STUDIES: StableOrHeritableRegulatoryStates
  AFFECTS: GeneActivity
  WITHOUT_REQUIRING: DNASequenceChange
  INCLUDES: [DNA_Methylation, HistoneModification, ChromatinRemodelling, RegulatoryRNA, EpigeneticInheritance]
}

ENTITY EpigeneticState {
  APPLIES_TO: [Gene, GenomicRegion, Chromatin]
  MAY_AFFECT: GeneExpression
  MAY_BE: [Stable, Dynamic, Reversible]
}

ENTITY Chromatin {
  COMPOSED_OF: [DNA, HistoneProtein]
  ORGANIZES: Genome
  HAS_STATE: ChromatinState
}

ENTITY ChromatinState {
  MAY_BE: [Accessible, Compact, ActiveAssociated, RepressedAssociated]
  MODULATES: DNAAccessibility
}

PROCESS DNA_Methylation {
  TARGET: DNA
  ADDS: MethylGroup
  CATALYSED_BY: DNA_Methyltransferase
  MAY_MODULATE: GeneExpression
}

PROCESS DNA_Demethylation {
  TARGET: MethylatedDNA
  REDUCES: DNA_Methylation
  MAY_BE: [Active, Passive]
}

ENTITY CpGSite {
  IS_A: DNASequenceContext
  MAY_BE_TARGET_OF: DNA_Methylation
}

ENTITY CpGIsland {
  CONTAINS: HighDensityOfCpGSites
  MAY_OCCUR_NEAR: Promoter
}

PROCESS HistoneModification {
  TARGET: Histone
  MAY_INCLUDE: [HistoneAcetylation, HistoneMethylation, HistonePhosphorylation, HistoneUbiquitination]
  MAY_MODULATE: ChromatinState
}

ENTITY Histone {
  IS_A: ChromatinProtein
  ASSOCIATES_WITH: DNA
}

ENTITY Nucleosome {
  COMPOSED_OF: [DNA, HistoneCore]
  IS_BASIC_UNIT_OF: Chromatin
}

ENTITY EpigeneticWriter { ADDS_OR_ESTABLISHES: EpigeneticModification }
ENTITY EpigeneticEraser { REMOVES_OR_REVERSES: EpigeneticModification }
ENTITY EpigeneticReader {
  RECOGNIZES: EpigeneticModification
  MAY_RECRUIT: RegulatoryComplex
}

PROCESS ChromatinRemodelling {
  TARGET: Chromatin
  CHANGES: [NucleosomePosition, NucleosomeComposition, DNAAccessibility]
  MAY_REQUIRE: ATP
}

ENTITY RegulatoryRNA {
  IS_A: RNA
  MAY_MODULATE: [GeneExpression, ChromatinState, RNAStability, Translation]
}

CLASS miRNA { SUBCLASS_OF: RegulatoryRNA; MAY_REPRESS: TargetRNA }
CLASS siRNA { SUBCLASS_OF: RegulatoryRNA; MAY_DIRECT: RNAInterference }
CLASS lncRNA {
  SUBCLASS_OF: RegulatoryRNA
  MAY_INTERACT_WITH: [Chromatin, Protein, RNA]
  MAY_MODULATE: GeneExpression
}

PROCESS EpigeneticRegulation {
  TARGET: GeneExpression
  MAY_ACT_THROUGH: [DNAAccessibility, PromoterState, EnhancerState, TranscriptionFactorAccess, RegulatoryRNA]
}

PROCESS EpigeneticInheritance {
  TRANSMITS: EpigeneticState
  ACROSS: CellDivisionOrGeneration
  MAY_INCLUDE: [MitoticInheritance, TransgenerationalInheritance]
}

PROCESS GenomicImprinting {
  IS_A: ParentOfOriginDependentEpigeneticRegulation
  AFFECTS: AllelicExpression
}

PROCESS XChromosomeInactivation {
  IS_A: ChromosomeScaleEpigeneticRegulation
  REDUCES: -ExpressionFromSelectedXChromosome
}

PROCESS EpigeneticReprogramming {
  RESETS_OR_RECONFIGURES: EpigeneticState
  MAY_OCCUR_DURING: Development
}

ENTITY Epigenome {
  REPRESENTS: GenomeWideEpigeneticState
  INCLUDES: [DNA_MethylationPattern, HistoneModificationPattern, ChromatinAccessibility, ChromatinOrganization]
  DEPENDS_ON: [CellType, DevelopmentalStage, Environment]
}

PROCESS EpigeneticMeasurement {
  TARGET: EpigeneticFeature
  MAY_USE: [BisulfiteSequencing, ChIP_Sequencing, ATAC_Sequencing, ChromatinConformationAssay, SingleCellEpigenomics]
}

ENTITY ExperimentalContext {
  MAY_INCLUDE: [organism, tissue, cell_type, developmental_stage, treatment, timepoint, assay, replicate]
}

RULE PromoterMethylationRule {
  IF promoter_methylation INCREASES
  THEN transcription MAY_DECREASE
  WITH effect := context_dependent
}

RULE AccessibilityRule {
  IF ChromatinAccessibility INCREASES
  THEN regulatory_factor_access MAY_INCREASE
}

RULE ExpressionRegulationRule {
  IF EpigeneticState changes_at RegulatoryRegion
  THEN GeneExpression MAY_CHANGE
  WITH direction := evidence_and_context_dependent
}

RULE AssociationRule {
  IF EpigeneticModification correlates_with GeneExpressionChange
  THEN association := supported
  AND causality := unresolved
}

RULE CausalityRule {
  IF targeted_epigenetic_perturbation reproducibly_changes GeneExpression
  THEN causal_support := increase(causal_support)
}

RULE SequenceDistinction {
  IF EpigeneticState changes
  THEN DO_NOT_INFER DNASequenceChange
  UNLESS sequence_evidence EXISTS
}

ENTITY Evidence {
  TYPES: [EpigenomicEvidence, MolecularEvidence, GeneticEvidence, BiochemicalEvidence, ExpressionEvidence, DevelopmentalEvidence, SingleCellEvidence, ComputationalEvidence, LiteratureEvidence]
}

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

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

RELATION EpigeneticModification AFFECTS ChromatinState
RELATION ChromatinState MODULATES DNAAccessibility
RELATION DNAAccessibility MODULATES GeneExpression
RELATION DNA_Methylation MODIFIES DNA
RELATION HistoneModification MODIFIES Histone
RELATION ChromatinRemodelling MODIFIES ChromatinOrganization
RELATION RegulatoryRNA MODULATES GeneExpression
RELATION Epigenome ASSOCIATED_WITH CellIdentity
RELATION EpigeneticState MAY_BE_INHERITED_BY EpigeneticInheritance

SEMANTIC_EQUIVALENCE {
  "epigenetic mark" ~= "epigenetic modification" WHEN context == molecular_mark
  "chromatin accessibility" ~= "DNA accessibility within chromatin"
  "epigenomic profile" ~= "epigenome state profile" WHEN biological_context_is_defined
  "DNA methylation pattern" ~= "methylome pattern" WHEN genome_wide_context
}

CONFIDENCE EpigeneticAssertion {
  INPUTS: [assay_quality, biological_replication, molecular_support, epigenomic_support, expression_support, intervention_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"
}

QUERY EpigeneticStateLookup(genomic_region, biological_context) {
  RETURN [DNA_methylation, histone_modifications, chromatin_accessibility, chromatin_state, regulatory_RNA_associations, gene_expression_associations, assay_context, evidence, confidence]
}

QUERY GeneEpigeneticsLookup(gene_identifier, biological_context) {
  RETURN [promoter_state, enhancer_state, DNA_methylation, histone_modifications, chromatin_accessibility, expression_level, regulatory_factors, evidence, confidence]
}

QUERY EpigenomeComparison(context_a, context_b) {
  RETURN [differential_methylation, differential_histone_marks, differential_accessibility, affected_genes, expression_associations, uncertainty, evidence, confidence]
}

UPDATE_MODEL {
  ON new_epigenetic_evidence:
    validate_provenance()
    identify_organism()
    identify_genome_assembly()
    normalize_genomic_coordinates()
    normalize_gene_identifiers()
    capture_cell_type()
    capture_developmental_stage()
    capture_environmental_context()
    identify_assay()
    normalize_epigenetic_measurements()
    compare_existing_assertions()
    preserve_conflicting_evidence()
    recalculate_confidence()
    regenerate_regulatory_links()
    update_flow_hash()
}

AI_CONSUMPTION {
  MODE: FormalSemanticReasoning
  PARSE_AS: ExecutableFlowAlgebra
  PRIORITIES: [epigenetic_feature_identity, genomic_location, chromatin_context, cell_type, developmental_stage, gene_expression_context, assay_context, evidence_provenance, confidence, semantic_equivalence]
  REQUIREMENTS: [
    distinguish_epigenetic_change_from_DNA_sequence_change,
    distinguish_association_from_causation,
    preserve_species_context,
    preserve_genome_assembly,
    preserve_cell_type_and_tissue_context,
    preserve_developmental_context,
    preserve_environmental_context,
    preserve_assay_method,
    distinguish_stable_from_transient_state,
    avoid_unsupported_transgenerational_inference
  ]
}

VALIDATE {
  REQUIRE Epigenetics
  REQUIRE EpigeneticState
  REQUIRE Chromatin
  REQUIRE DNA_Methylation
  REQUIRE HistoneModification
  REQUIRE ChromatinRemodelling
  REQUIRE Epigenome
  REQUIRE EpigeneticMeasurement
  REQUIRE Evidence
  REQUIRE CONFIDENCE
  REQUIRE SEMANTIC_EQUIVALENCE
  REQUIRE UPDATE_MODEL
  REQUIRE AI_CONSUMPTION

  ASSERT EpigeneticState != DNASequence
  ASSERT DNA_Methylation TARGET == DNA
  ASSERT HistoneModification TARGET == Histone
  ASSERT association != causation
}

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 "EpigeneticsOntology"