Euchromatin Ontology

FLOW ALGEBRA
EUCHROMATIN ONTOLOGY
Kireth Semantic Library | Biological Entities > Gene Expression Entities
Version: 1.0 | Date: 2026-10-15 | Encoding: UTF-8
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/gene-expression-entities/euchromatin-ontology.html
Status: Domain-grounded formalisation; source chapter not independently verified.
Authors: Mark Higgins — Sky (Recursive AI)

01. PURPOSE
flow "EuchromatinOntology" v1.0
  objective: represent euchromatin as a context-dependent, relatively accessible chromatin state
  scope: molecular structure, epigenetic signatures, transcriptional potential, transitions and evidence
  principle: accessibility does not guarantee active transcription

02. ENTITY TYPES
entity ChromatinRegion: {id:str, genome_build:str?, chromosome:str?, start:int?, end:int?, strand:str?}
entity EuchromatinState: {region:ChromatinRegion, cell_type:str, condition:str?, timepoint:str?, confidence:float}
entity HeterochromatinState: {region:ChromatinRegion, cell_type:str, confidence:float}
entity Nucleosome: {id:str, histone_octamer:bool, dna_wrapped:bool}
entity HistoneModification: {mark:str, position:str?, abundance:float?, assay:str?}
entity DNAAccessibility: {region:ChromatinRegion, score:float, method:str}
entity DNAMethylation: {region:ChromatinRegion, fraction:float?, context:str?}
entity TranscriptionUnit: {gene_id:str, region:ChromatinRegion, expression:float?, units:str?}
entity RegulatoryElement: {id:str, kind:enum(promoter,enhancer,other), region:ChromatinRegion}
entity TranscriptionFactor: {id:str, binding_site:ChromatinRegion?}
entity ChromatinRemodeller: {id:str, complex_name:str?}
entity EpigeneticObservation: {sample_id:str, assay:str, measurement:float?, provenance:str}
entity BiologicalContext: {organism:str, tissue:str?, cell_type:str?, developmental_stage:str?, condition:str?}

03. TYPE HIERARCHY
ChromatinState > EuchromatinState
ChromatinState > HeterochromatinState
ChromatinRegion contains Nucleosome
ChromatinRegion overlaps RegulatoryElement
ChromatinRegion may_overlap TranscriptionUnit

04. RELATIONSHIP TYPES
relation has_state(ChromatinRegion, ChromatinState)
relation contains_nucleosome(ChromatinRegion, Nucleosome)
relation carries_mark(ChromatinRegion, HistoneModification)
relation exhibits_accessibility(ChromatinRegion, DNAAccessibility)
relation overlaps_gene(ChromatinRegion, TranscriptionUnit)
relation overlaps_regulatory_element(ChromatinRegion, RegulatoryElement)
relation binds_factor(RegulatoryElement, TranscriptionFactor)
relation remodelled_by(ChromatinRegion, ChromatinRemodeller)
relation measured_by(ChromatinRegion, EpigeneticObservation)
relation observed_in(ChromatinState, BiologicalContext)
relation transitions_to(ChromatinState, ChromatinState)
relation supports_inference(EpigeneticObservation, ChromatinState)

05. BIOLOGICAL CHARACTERISTICS
property relative_compaction: generally lower than constitutive heterochromatin
property nucleosome_organisation: variable; locally depleted at many active regulatory elements
property transcriptional_potential: often permissive, not necessarily actively transcribed
property replication_timing: often early, but not an absolute diagnostic criterion
property histone_marks: H3K4me3 commonly associated with active promoters
property histone_marks: H3K27ac commonly associated with active promoters and enhancers
property histone_marks: H3K36me3 commonly associated with transcribed gene bodies
property dna_methylation: context dependent; unmethylated CpG-rich promoters frequently accessible
property dynamics: reversible or persistent depending on cell identity and regulation

06. CLASSIFICATION RULES
rule E1:
  IF accessible(region, context) AND active_promoter_marks(region, context)
  THEN candidate_euchromatin(region, context)
  confidence: evidence_weighted
rule E2:
  IF accessible(region, context) AND expression(gene, context) = low
  THEN retain_euchromatin_candidate(region, context)
  note: accessibility is not synonymous with expression
rule E3:
  IF H3K9me3_enrichment(region) AND low_accessibility(region)
  THEN candidate_heterochromatin(region, context)
  note: signatures are suggestive, not definitive
rule E4:
  IF assays_disagree(region)
  THEN classification_status(region) = uncertain
rule E5:
  IF cell_type_changes OR condition_changes
  THEN recompute_state(region, context)

07. EVIDENCE INTEGRATION
input ATAC_seq: accessibility evidence
input DNase_seq: accessibility evidence
input ChIP_seq: histone mark or factor occupancy evidence
input CUT_and_RUN: chromatin-associated protein evidence
input CUT_and_Tag: chromatin mark evidence
input RNA_seq: transcriptional output evidence
input bisulfite_sequencing: DNA methylation evidence
input microscopy: spatial compaction evidence, resolution-dependent
constraint: measurements must specify organism, reference genome, cell context, assay and controls
constraint: coordinate comparisons require matching genome builds or validated liftover

08. TRANSITION MODEL
state closed_or_compacted -> intermediate -> accessible
transition opening:
  may_involve: pioneer_factor_binding, nucleosome_remodelling, histone_modification
  result: increased accessibility in specified context
transition closing:
  may_involve: loss_of_activators, repressive_modifications, nucleosome_repositioning
  result: decreased accessibility in specified context
constraint: transitions are not universally linear or irreversible

09. GENE EXPRESSION FLOW
flow gene_expression_potential:
  input: ChromatinRegion, BiologicalContext
  assess: accessibility
  assess: promoter_and_enhancer_status
  assess: transcription_factor_availability
  assess: RNA_polymerase_recruitment
  assess: observed_transcription
  output: {state_prediction, expression_potential, evidence, uncertainty}
  rule: open_chromatin != guaranteed_transcription

10. SEMANTIC RELATIONSHIPS
SEMANTIC_EQUIVALENCE:
  "open chromatin" ~ "accessible chromatin" [contextual, not strict synonym for euchromatin]
  "euchromatin" != "actively transcribed DNA"
  "euchromatin" != "unmodified histones"
  "heterochromatin" != "permanently silent DNA"
  "H3K27ac" != "proof of transcription"
  "histone acetylation" != "universal chromatin activation"

11. RECURSIVE REASONING
recursive infer_state(region, context, depth):
  if depth > max_depth: return unresolved
  observations = collect_evidence(region, context)
  candidates = evaluate_rules(observations)
  conflicts = detect_conflicting_evidence(candidates)
  if conflicts: request_orthogonal_assays_or_context_review()
  return calibrated_classification(candidates, conflicts)
termination: max_depth and visited_entity_set
invariant: no inference may overwrite primary experimental evidence

12. CONFIDENCE
CONFIDENCE:
  range: [0.0, 1.0]
  dimensions: assay_quality, reproducibility, cell_type_match, genome_build_match, orthogonal_support
  calculation: calibrated_model_or_explicit_weighted_evidence
  missing_data: unknown_not_false
  contradictory_data: reduce_confidence_and_record_conflict
  uncertainty: report_probability_only_if_calibrated

13. PROVENANCE AND VALIDATION
validation required:
  - coordinates satisfy 0 <= start < end where provided
  - genomic assembly and species are explicit for mapped observations
  - biological context accompanies chromatin-state claims
  - assay names and experimental controls are recorded
  - inferential and directly measured assertions are distinguished
  - no universal claim from a single cell type
provenance: {source_id, dataset_id?, assay, date?, evidence_level, curator?}

14. FLOW_HASH
FLOW_HASH:
  algorithm: SHA-256
  canonicalise: UTF-8, LF newlines, stable field ordering
  digest_input: canonical_flow_payload_excluding_flow_hash_field
  value: compute_at_publication
  purpose: version integrity and reproducible comparison

15. UPDATE_MODEL
UPDATE_MODEL:
  trigger: new_assay | corrected_annotation | new_genome_assembly | new_evidence | revised_definition
  steps:
    - preserve_previous_version
    - validate_new_evidence
    - reconcile_coordinates_and_context
    - recalculate_inferences_and_confidence
    - record_change_log_and_provenance
    - regenerate_FLOW_HASH
  policy: never silently replace conflicting observations

16. AI_CONSUMPTION
AI_CONSUMPTION:
  format: typed semantic graph + machine-readable flow rules
  primary_entity: EuchromatinState
  context_required: organism, cell_type, experimental_condition
  reasoning_modes: classification, relationship_traversal, evidence_synthesis, state_transition
  outputs: {classification, related_entities, confidence, evidence, provenance, limitations}
  safeguards:
    - avoid treating correlation as causation
    - distinguish accessible chromatin from active transcription
    - avoid extrapolating across tissues or species without evidence
    - preserve ambiguity and assay limitations

17. EXAMPLE INSTANCE (ILLUSTRATIVE, NOT EMPIRICAL)
example:
  region: demo_region_001
  context: demo_cell_type
  evidence: {ATAC_accessibility: high, H3K27ac: enriched, RNA_expression: unknown}
  inferred_state: candidate_euchromatin
  confidence: not_calibrated
  interpretation: accessible regulatory chromatin is plausible; transcription unconfirmed

18. LINKED ONTOLOGIES
links:
  - Chromatin Ontology
  - Heterochromatin Ontology
  - Histone Ontology
  - Epigenetic Marker Ontology
  - Methylated DNA Ontology
  - Gene Expression Entity Ontology
  - Regulatory Network Entity Ontology
  - Transcription Factor Ontology
  - RNA Polymerase Ontology

END FLOW ALGEBRA