Transcription Ontology

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

flow "TranscriptionOntology" v1.0

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

ENTITY TranscriptionOntology {
    TYPE: BiologicalOntology
    DOMAIN: MolecularBiology
    SUBJECT: Transcription
    PURPOSE: FormalSemanticRepresentation
}

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

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

PROCESS Transcription {
    IS_A: GeneExpressionProcess
    INPUT: DNA
    TEMPLATE: DNA_TemplateStrand
    CATALYSED_BY: RNA_Polymerase
    OUTPUT: RNA
    DIRECTION_OF_RNA_SYNTHESIS: "5-prime to 3-prime"
}

ENTITY DNA {
    IS_A: NucleicAcid
    CONTAINS: Gene
    PROVIDES: TranscriptionTemplate
}

ENTITY DNA_TemplateStrand {
    PART_OF: DNA
    READ_BY: RNA_Polymerase
    DIRECTION_OF_READING: "3-prime to 5-prime"
}

ENTITY CodingStrand {
    PART_OF: DNA
    CORRESPONDS_TO: RNASequence
    DIFFERENCE_FROM_RNA: "T in DNA corresponds to U in RNA"
}

ENTITY RNA {
    IS_A: NucleicAcid
    PRODUCED_BY: Transcription
    MAY_BE: [mRNA, rRNA, tRNA, RegulatoryRNA, OtherRNA]
}

ENTITY RNA_Polymerase {
    IS_A: Enzyme
    CATALYSES: RNA_Synthesis
    USES_TEMPLATE: DNA_TemplateStrand
}

# ============================================================
# TRANSCRIPTION UNIT
# ============================================================

ENTITY TranscriptionUnit {
    MAY_INCLUDE: [
        Promoter,
        TranscriptionStartSite,
        TranscribedRegion,
        Terminator
    ]
    PRODUCES: RNA
}

ENTITY Promoter {
    IS_A: RegulatoryDNARegion
    ASSOCIATED_WITH: TranscriptionInitiation
    BINDS_OR_RECRUITS: TranscriptionMachinery
}

ENTITY TranscriptionStartSite {
    MARKS: RNA_SynthesisStartPosition
    ASSOCIATED_WITH: Promoter
}

ENTITY TranscribedRegion {
    PART_OF: TranscriptionUnit
    COPIED_INTO: RNA
}

ENTITY Terminator {
    IS_A: DNASequenceOrSignal
    ASSOCIATED_WITH: TranscriptionTermination
}

RELATION Gene MAY_HAVE Promoter
RELATION Promoter PRECEDES TranscribedRegion
RELATION TranscriptionStartSite STARTS TranscribedRegion
RELATION Terminator MAY_END TranscriptionUnit

# ============================================================
# TRANSCRIPTION STAGES
# ============================================================

PROCESS TranscriptionInitiation {
    SUBPROCESS_OF: Transcription
    REQUIRES: [
        PromoterRecognition,
        TranscriptionMachineryAssembly,
        DNA_LocalUnwinding
    ]
    OUTPUT: InitiatedTranscriptionComplex
}

PROCESS TranscriptionElongation {
    SUBPROCESS_OF: Transcription
    EXTENDS: RNA_Transcript
    USES: RibonucleosideTriphosphate
}

PROCESS TranscriptionTermination {
    SUBPROCESS_OF: Transcription
    STOPS: RNA_Synthesis
    RELEASES: RNA_Transcript
}

RULE StageOrder {
    TranscriptionInitiation
        -> TranscriptionElongation
        -> TranscriptionTermination
}

# ============================================================
# INITIATION
# ============================================================

ENTITY TranscriptionFactor {
    IS_A: RegulatoryProtein
    MAY_BIND: DNA
    MAY_MODULATE: Transcription
}

ENTITY GeneralTranscriptionFactor {
    SUBCLASS_OF: TranscriptionFactor
    CONTRIBUTES_TO: BasalTranscriptionInitiation
}

ENTITY InitiationComplex {
    COMPOSED_OF: [RNA_Polymerase, RequiredFactors]
    ASSEMBLES_AT: Promoter
}

RULE InitiationRule {
    IF Promoter IS_RECOGNIZED
       AND required_transcription_machinery IS_ASSEMBLED
    THEN RNA_Polymerase MAY_INITIATE RNA_Synthesis
}

# ============================================================
# ELONGATION
# ============================================================

ENTITY TranscriptionBubble {
    IS_A: LocallyUnwoundDNARegion
    ASSOCIATED_WITH: ActiveRNA_Polymerase
}

ENTITY NascentRNA {
    IS_A: GrowingRNAChain
    PRODUCED_DURING: TranscriptionElongation
}

RULE BasePairingRule {
    IF DNA_TemplateBase == A THEN RNA_Base := U
    IF DNA_TemplateBase == T THEN RNA_Base := A
    IF DNA_TemplateBase == C THEN RNA_Base := G
    IF DNA_TemplateBase == G THEN RNA_Base := C
}

RULE ElongationRule {
    WHILE RNA_Polymerase progresses_along DNA_TemplateStrand:
        SELECT complementary_ribonucleotide
        FORM phosphodiester_bond
        EXTEND NascentRNA in "5-prime to 3-prime" direction
}

# ============================================================
# TERMINATION
# ============================================================

ENTITY TerminationSignal {
    CAUSES_OR_PROMOTES: TranscriptionTermination
}

RULE TerminationRule {
    IF RNA_Polymerase ENCOUNTERS applicable_TerminationSignal
    THEN {
        STOP RNA_elongation
        RELEASE RNA_Transcript
        DISSOCIATE_OR_RECYCLE transcription_complex
    }
}

# ============================================================
# PROKARYOTIC TRANSCRIPTION
# ============================================================

PROCESS ProkaryoticTranscription {
    SUBCLASS_OF: Transcription
    OCCURS_IN: ProkaryoticCell
    MAY_PRODUCE: PolycistronicRNA
}

ENTITY SigmaFactor {
    IS_A: TranscriptionInitiationFactor
    ASSOCIATED_WITH: BacterialRNA_Polymerase
    CONTRIBUTES_TO: PromoterRecognition
}

ENTITY Operon {
    IS_A: TranscriptionalRegulatoryUnit
    MAY_CONTAIN: MultipleGenes
    MAY_PRODUCE: PolycistronicRNA
}

RULE ProkaryoticInitiationRule {
    IF SigmaFactor DIRECTS RNA_Polymerase TO compatible_Promoter
    THEN TranscriptionInitiation MAY_OCCUR
}

# ============================================================
# EUKARYOTIC TRANSCRIPTION
# ============================================================

PROCESS EukaryoticTranscription {
    SUBCLASS_OF: Transcription
    OCCURS_IN: EukaryoticCell
    REQUIRES: ChromatinContext
}

ENTITY RNA_Polymerase_I {
    SUBCLASS_OF: RNA_Polymerase
    TRANSCRIBES_PRIMARILY: RibosomalRNA_Genes
}

ENTITY RNA_Polymerase_II {
    SUBCLASS_OF: RNA_Polymerase
    TRANSCRIBES_PRIMARILY: ProteinCodingGenesAndSelectedNonCodingRNAs
}

ENTITY RNA_Polymerase_III {
    SUBCLASS_OF: RNA_Polymerase
    TRANSCRIBES_PRIMARILY: tRNA_AndSelectedSmallRNAs
}

ENTITY Enhancer {
    IS_A: RegulatoryDNARegion
    MAY_INCREASE: Transcription
}

ENTITY Silencer {
    IS_A: RegulatoryDNARegion
    MAY_DECREASE: Transcription
}

# ============================================================
# TRANSCRIPTIONAL REGULATION
# ============================================================

PROCESS TranscriptionalRegulation {
    TARGET: TranscriptionRate
    MAY_USE: [
        Activator,
        Repressor,
        Enhancer,
        Silencer,
        ChromatinModification,
        DNA_Methylation
    ]
}

ENTITY Activator {
    SUBCLASS_OF: TranscriptionFactor
    MAY_INCREASE: Transcription
}

ENTITY Repressor {
    SUBCLASS_OF: TranscriptionFactor
    MAY_DECREASE: Transcription
}

RULE ActivationRule {
    IF Activator BINDS compatible_RegulatoryRegion
    THEN transcription_probability_or_rate MAY_INCREASE
}

RULE RepressionRule {
    IF Repressor BINDS compatible_RegulatoryRegion
    THEN transcription_probability_or_rate MAY_DECREASE
}

# ============================================================
# CHROMATIN AND EPIGENETIC CONTEXT
# ============================================================

ENTITY Chromatin {
    COMPOSED_OF: [DNA, Protein]
    MAY_EXIST_AS: [AccessibleChromatin, CompactChromatin]
}

ENTITY HistoneModification {
    IS_A: EpigeneticModification
    MAY_CHANGE: ChromatinAccessibility
}

ENTITY DNA_Methylation {
    IS_A: EpigeneticModification
    MAY_MODULATE: Transcription
}

RULE ChromatinAccessibilityRule {
    IF PromoterAccessibility INCREASES
    THEN transcriptional_access MAY_INCREASE
}

# ============================================================
# RNA PROCESSING RELATIONSHIP
# ============================================================

PROCESS RNAProcessing {
    OCCURS_AFTER_OR_DURING: Transcription
    MAY_INCLUDE: [
        FivePrimeCapping,
        RNA_Splicing,
        Polyadenylation,
        RNAEditing
    ]
}

ENTITY PrimaryTranscript {
    PRODUCED_BY: Transcription
    MAY_REQUIRE: RNAProcessing
}

ENTITY MatureRNA {
    DERIVED_FROM: PrimaryTranscript
}

RELATION Transcription PRODUCES PrimaryTranscript
RELATION PrimaryTranscript PROCESSED_TO MatureRNA

RULE ProcessingDistinction {
    IF process == RNAProcessing
    THEN process != Transcription
    AND maintain_process_boundary()
}

# ============================================================
# TRANSCRIPTION FIDELITY
# ============================================================

ENTITY TranscriptionError {
    OCCURS_DURING: RNA_Synthesis
    AFFECTS: RNASequence
    DOES_NOT_NECESSARILY_CHANGE: DNASequence
}

RULE FidelityRule {
    IF RNA_Base DOES_NOT_MATCH expected_complement_of(DNA_TemplateBase)
    THEN TranscriptionError := true
}

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

ENTITY TranscriptionFunction {
    DIMENSIONS: [
        GeneticInformationTransfer,
        GeneExpression,
        RNAProduction,
        RegulatoryControl
    ]
}

RELATION Transcription TRANSFERS_INFORMATION_FROM DNA TO RNA
RELATION Transcription CONTRIBUTES_TO GeneExpression
RELATION Transcription PRODUCES RNA
RELATION Transcription REGULATED_BY TranscriptionalRegulation

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

ENTITY Evidence {
    TYPES: [
        MolecularEvidence,
        BiochemicalEvidence,
        SequencingEvidence,
        ExpressionEvidence,
        GeneticEvidence,
        ComputationalEvidence,
        LiteratureEvidence
    ]
}

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

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

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

RELATION Gene TRANSCRIBED_TO RNA
RELATION DNA_TemplateStrand TEMPLATE_FOR RNA
RELATION RNA_Polymerase CATALYSES Transcription
RELATION Promoter REGULATES TranscriptionInitiation
RELATION TranscriptionFactor REGULATES Transcription
RELATION Transcription PRODUCES RNA
RELATION RNAProcessing MODIFIES PrimaryTranscript
RELATION Transcription PART_OF GeneExpression

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

SEMANTIC_EQUIVALENCE {
    "transcription" ~= "RNA synthesis from DNA template"
    "template strand" ~= "antisense strand" WHEN context == specific_transcription_unit
    "coding strand" ~= "sense strand" WHEN context == specific_transcription_unit
    "primary transcript" ~= "initial RNA transcript"
    "transcription start site" ~= "RNA synthesis initiation position"
}

RULE EquivalenceConstraint {
    IF terms ARE semantic_equivalents
    THEN preserve_gene_context()
    AND preserve_strand_orientation()
    AND preserve_organism_context()
    AND preserve_polymerase_context()
    AND prevent_false_identity()
}

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

CONFIDENCE TranscriptionAssertion {
    INPUTS: [
        molecular_support,
        biochemical_support,
        sequencing_support,
        expression_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 TranscriptInference {
    IF RNA_Polymerase TRANSCRIBES DNA_TemplateStrand
    THEN RNA.sequence := complement_with_U(DNA_TemplateStrand.sequence)
}

RULE GeneExpressionInference {
    IF Gene IS_TRANSCRIBED
    THEN GeneExpression HAS_STAGE Transcription
}

RULE PromoterInference {
    IF DNARegion RECRUITS transcription_machinery
       AND initiates_transcription_at_associated_site
    THEN DNARegion MAY_BE Promoter
}

RULE RegulatoryInference {
    IF Factor binding CHANGES transcription_rate
    THEN Factor MAY_BE TranscriptionalRegulator
}

RULE RNAProductInference {
    IF TranscriptionUnit IS_TRANSCRIBED
    THEN EXISTS RNA_Transcript
    WITH identity := transcription_unit_specific
}

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

QUERY TranscriptionLookup(gene_or_transcription_unit) {
    RETURN [
        identity,
        promoter,
        transcription_start_site,
        template_strand,
        coding_strand,
        RNA_polymerase,
        transcription_factors,
        regulatory_elements,
        transcript,
        termination_signal,
        evidence,
        confidence
    ]
}

QUERY PromoterLookup(promoter_identifier) {
    RETURN [
        associated_gene,
        sequence,
        transcription_start_site,
        bound_factors,
        polymerase_context,
        regulatory_evidence,
        confidence
    ]
}

QUERY TranscriptLookup(transcript_identifier) {
    RETURN [
        source_gene,
        transcription_unit,
        primary_sequence,
        processing_state,
        transcript_type,
        evidence,
        confidence
    ]
}

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

UPDATE_MODEL {
    ON new_transcription_evidence:
        validate_provenance()
        identify_organism()
        normalize_gene_identifier()
        normalize_transcript_identifier()
        establish_strand_orientation()
        identify_polymerase_context()
        map_promoters_and_regulatory_elements()
        record_experimental_conditions()
        compare_existing_assertions()
        preserve_conflicting_evidence()
        recalculate_confidence()
        regenerate_semantic_links()
        update_flow_hash()
}

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

AI_CONSUMPTION {
    MODE: FormalSemanticReasoning
    PARSE_AS: ExecutableFlowAlgebra

    PRIORITIES: [
        transcription_unit_identity,
        strand_orientation,
        promoter_context,
        polymerase_identity,
        RNA_product_identity,
        regulatory_context,
        evidence_provenance,
        confidence,
        semantic_equivalence
    ]

    REQUIREMENTS: [
        distinguish_transcription_from_replication,
        distinguish_transcription_from_translation,
        distinguish_template_strand_from_coding_strand,
        preserve_sequence_direction,
        preserve_species_context,
        preserve_polymerase_context,
        distinguish_primary_from_mature_transcript,
        distinguish_observed_from_inferred_regulation,
        avoid_unsupported_causal_inference
    ]
}

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

VALIDATE {
    REQUIRE Transcription
    REQUIRE DNA
    REQUIRE RNA
    REQUIRE RNA_Polymerase
    REQUIRE Promoter
    REQUIRE TranscriptionInitiation
    REQUIRE TranscriptionElongation
    REQUIRE TranscriptionTermination
    REQUIRE Evidence
    REQUIRE CONFIDENCE
    REQUIRE SEMANTIC_EQUIVALENCE
    REQUIRE UPDATE_MODEL
    REQUIRE AI_CONSUMPTION

    ASSERT Transcription INPUT == DNA
    ASSERT Transcription OUTPUT == RNA
    ASSERT RNA_Polymerase CATALYSES Transcription
    ASSERT DNA_TemplateStrand != CodingStrand
    ASSERT Transcription != Translation
    ASSERT Transcription != DNAReplication
}

# ============================================================
# 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 "TranscriptionOntology"