RNA Polymerase Ontology

FLOW ALGEBRA
RNA POLYMERASE ONTOLOGY
Kireth Semantic Library | Gene Expression Entities
Authors: Mark Higgins — Sky (Recursive AI)
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/gene-expression-entities/rna-polymerase-ontology.html
Version: 1.0 | Date: 2026-10-15 | Encoding: UTF-8
Status: Domain-grounded formalisation; source page's embedded specification not available in retrieved text.

AI_INTERPRETATION:
  Treat the declarations below as typed semantic constraints and inference rules.
  Biological assertions are context-sensitive, not universal across taxa.
  Do not infer a mechanism from a name alone.

flow "RNAPolymeraseOntology" v1.0 {

  DOMAIN:
    ontology_id: "KIRETH:GENE_EXPRESSION:RNA_POLYMERASE"
    parent: "GeneExpressionEntityOntology"
    subject: "RNA polymerase enzymes and transcription machinery"
    scope: [bacteria, archaea, eukaryotes, organelles, viruses]

  TYPES:
    Entity := {id:str, label:str, taxon:str?, provenance:str?}
    Polymerase <: Entity
    DNA_Dependent_RNAPolymerase <: Polymerase
    RNA_Dependent_RNAPolymerase <: Polymerase
    PolymeraseSubunit <: Entity
    TranscriptionFactor <: Entity
    SigmaFactor <: TranscriptionFactor
    Promoter <: Entity
    DNA_Template <: Entity
    RNA_Template <: Entity
    RNA_Transcript <: Entity
    NucleotideTriphosphate <: Entity
    TranscriptionComplex <: Entity
    TerminationSignal <: Entity
    Evidence <: Entity
    Observation <: Entity
    Context := {taxon:str?, compartment:str?, condition:str?, stage:str?}
    Confidence := real[0,1]

  CLASSIFICATION:
    bacterial_core_RNAP: DNA_Dependent_RNAPolymerase
    bacterial_holoenzyme: TranscriptionComplex
    archaeal_RNAP: DNA_Dependent_RNAPolymerase
    eukaryotic_RNAP_I: DNA_Dependent_RNAPolymerase
    eukaryotic_RNAP_II: DNA_Dependent_RNAPolymerase
    eukaryotic_RNAP_III: DNA_Dependent_RNAPolymerase
    plant_RNAP_IV: DNA_Dependent_RNAPolymerase
    plant_RNAP_V: DNA_Dependent_RNAPolymerase
    mitochondrial_RNAP: DNA_Dependent_RNAPolymerase
    viral_RdRp: RNA_Dependent_RNAPolymerase

  RELATIONS:
    IS_A(Entity, Entity)
    HAS_SUBUNIT(Polymerase, PolymeraseSubunit)
    FORMS_COMPLEX_WITH(Polymerase, Entity)
    RECOGNISES_PROMOTER(TranscriptionComplex, Promoter, Context)
    BINDS_TEMPLATE(Polymerase, Entity, Context)
    INITIATES_AT(Polymerase, Promoter, Context)
    CATALYSES(Polymerase, str, Context)
    PRODUCES(Polymerase, RNA_Transcript, Context)
    REGULATED_BY(Polymerase, Entity, Context)
    LOCALISED_IN(Polymerase, str, Context)
    SUPPORTED_BY(str, Evidence)

  AXIOMS:
    A1: DNA_Dependent_RNAPolymerase IS_A Polymerase
    A2: RNA_Dependent_RNAPolymerase IS_A Polymerase
    A3: DNA-dependent RNA polymerases use DNA as template.
    A4: RNA-dependent RNA polymerases use RNA as template.
    A5: RNA synthesis extends the RNA 3-prime end, producing RNA 5-prime to 3-prime.
    A6: RNA synthesis consumes ribonucleoside triphosphates and releases pyrophosphate.
    A7: Promoter recognition, initiation and termination differ among biological systems.
    A8: A polymerase classification does not imply an identical subunit composition across taxa.
    A9: Polymerase presence does not by itself establish active transcription.

  TRANSCRIPTION_STATES:
    states: [unbound, recruited, initiation_complex, initiating,
             promoter_escape, elongating, paused, terminating, released]
    transitions:
      unbound -> recruited: recruitment_or_promoter_recognition
      recruited -> initiation_complex: complex_assembly_and_template_opening
      initiation_complex -> initiating: first_phosphodiester_bonds
      initiating -> promoter_escape: stable_productive_elongation
      promoter_escape -> elongating: processive_RNA_synthesis
      elongating -> paused: pausing_signal_or_regulator
      paused -> elongating: pause_release
      elongating -> terminating: termination_pathway
      terminating -> released: transcript_and_polymerase_release
    constraints:
      - transitions require organism- and mechanism-specific evidence
      - initiation may be abortive and need not reach promoter_escape
      - elongation may involve backtracking and proofreading

  REACTION:
    input: RNA_chain_n + NTP
    output: RNA_chain_n_plus_1 + PPi
    direction: 5_prime_to_3_prime
    template_reading: 3_prime_to_5_prime
    prerequisite: suitable_template_and_catalytic_complex

  RULES:
    R01:
      IF enzyme IS_A DNA_Dependent_RNAPolymerase
      AND BINDS_TEMPLATE(enzyme, DNA_template, context)
      THEN potential_process(enzyme, DNA_directed_transcription, context)
    R02:
      IF enzyme IS_A RNA_Dependent_RNAPolymerase
      AND BINDS_TEMPLATE(enzyme, RNA_template, context)
      THEN potential_process(enzyme, RNA_directed_RNA_synthesis, context)
    R03:
      IF taxon = bacteria AND holoenzyme_contains(core_RNAP, sigma_factor)
      THEN sigma_factor_may_confer_promoter_specificity
    R04:
      IF taxon = eukaryote AND enzyme = RNAP_II
      THEN canonical_products_include(pre_mRNA, selected_non_coding_RNAs)
    R05:
      IF taxon = eukaryote AND enzyme = RNAP_I
      THEN canonical_product = large_rRNA_precursor
    R06:
      IF taxon = eukaryote AND enzyme = RNAP_III
      THEN canonical_products_include(tRNA, 5S_rRNA, selected_small_RNAs)
    R07:
      IF taxon = land_plant AND enzyme IN [RNAP_IV, RNAP_V]
      THEN associate_with(RNA_directed_DNA_methylation_pathways)
    R08:
      IF observed(transcriptional_activity) AND verified(template_identity)
      THEN classify_process_by_template_identity
    R09:
      IF promoter_binding_detected AND NOT initiation_detected
      THEN do_not_assert(productive_transcription)
    R10:
      IF inhibitor_effect_observed
      THEN infer_polymerase_specificity ONLY_IF selectivity_and_context_verified

  CONTEXTUAL_DISTINCTIONS:
    - bacterial RNAP uses sigma factors for many promoter recognition events
    - eukaryotic nuclear RNAP II initiation typically requires general transcription factors
    - archaeal transcription machinery shares important features with eukaryotic machinery
    - organellar RNA polymerases have lineage-specific origins and architectures
    - viral RNA-dependent RNA polymerases are distinct from cellular DNA-dependent RNAPs
    - some viruses encode DNA-dependent RNA polymerases; avoid universal viral classification
    - RNAP I/II/III product lists are canonical summaries, not exhaustive partitions

  EVIDENCE_MODEL:
    evidence_types: [biochemical_assay, structural_data, sequence_homology,
                     genetics, transcriptomics, microscopy, literature]
    require:
      - taxonomic_scope
      - assay_or_method
      - provenance
      - observation_vs_inference_distinction
    negative_result: absence_of_detection != demonstrated_absence

  CONFIDENCE:
    range: [0.0, 1.0]
    parameters: [source_reliability, experimental_support,
                 contextual_match, replication, conflicting_evidence]
    combine: calibrated_evidence_aggregation
    policy:
      - never fabricate numerical confidence
      - report unknown where evidence is insufficient
      - lower confidence for cross-taxon extrapolation
      - preserve competing interpretations when unresolved

  SEMANTIC_EQUIVALENCE:
    exact_aliases:
      "RNA polymerase": "RNAP" # generic name only
      "RNA polymerase II": "Pol II"
      "RNA-dependent RNA polymerase": "RdRp"
    prohibited_equivalences:
      - RNAP_II != all_RNA_polymerases
      - bacterial_RNAP != eukaryotic_RNAP_II
      - DNA_dependent_RNAP != RNA_dependent_RNAP
      - transcription_factor != RNA_polymerase
    equivalence_requires: same_referent_and_taxonomic_context

  GRAPH_INFERENCE:
    seed: Polymerase
    traverse: [IS_A, HAS_SUBUNIT, FORMS_COMPLEX_WITH,
               BINDS_TEMPLATE, PRODUCES, REGULATED_BY]
    depth_limit: 5
    cycle_policy: visited_entity_relation_context
    output: evidence_annotated_subgraph

  RECURSIVE_REASONING:
    step_1: identify_polymerase_and_taxon
    step_2: identify_template_and_subunits
    step_3: resolve_promoter_and_regulatory_context
    step_4: evaluate_initiation_elongation_termination_evidence
    step_5: connect_products_to_transcript_ontology
    step_6: propagate_evidence_and_uncertainty
    step_7: stop_at_fixed_point_or_depth_limit
    guard: do_not_convert_possible_mechanism_to_observed_fact

  FLOW_HASH:
    algorithm: SHA-256
    canonicalise: [ontology_id, version, types, relations, axioms,
                   rules, context, evidence, provenance]
    exclude: [runtime_timestamp, display_whitespace]
    output: computed_at_ingestion
    note: no_hash_value_claimed_without_execution

  UPDATE_MODEL:
    triggers: [new_experimental_evidence, taxonomy_revision,
               structural_reclassification, corrected_mechanism,
               source_revision]
    operations: [validate, version, diff, recompute_inferences,
                 recalculate_confidence, recompute_hash]
    preserve: [prior_versions, provenance, conflicting_claims]
    reject: unsupported_or_untraceable_updates

  AI_CONSUMPTION:
    mode: typed_semantic_reasoning
    input: [polymerase_entity, taxon, template, biological_context, evidence]
    output: [classification, molecular_relations, process_hypotheses,
             supported_conclusions, confidence, provenance]
    restrictions:
      - distinguish enzyme from holoenzyme and transcription complex
      - distinguish biological observation from inferred mechanism
      - require context for generalisations
      - do not invent sequence, kinetics, experiments or citations
      - preserve unknown and disputed states

  VALIDATION:
    V01: each entity has a unique stable identifier
    V02: each relation respects declared argument types
    V03: DNA-dependent and RNA-dependent polymerases are not conflated
    V04: product annotations carry taxonomic context
    V05: asserted activity requires supporting evidence
    V06: inferred relationships retain provenance
    V07: every numerical confidence is evidence-calibrated
    V08: recursive traversal terminates
    V09: FLOW_HASH is computed, never guessed

  OUTPUT_SCHEMA:
    ontology: str
    version: str
    entities: list[Entity]
    relationships: list[typed_relation]
    inferred_claims: list[claim_with_context]
    confidence: Confidence | unknown
    provenance: list[Evidence]
    flow_hash: str | pending_computation
    update_status: str
}

END FLOW ALGEBRA