Translation Ontology

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

flow "TranslationOntology" v1.0

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

ENTITY TranslationOntology {
    TYPE: BiologicalOntology
    DOMAIN: MolecularBiology
    SUBJECT: Translation
    PURPOSE: FormalSemanticRepresentation
}

PAGE {
    TITLE: "Translation Ontology"
    PARENT_DOMAIN: "Molecular Biology"
    CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/molecular-biology/translation-ontology-2.html"
    AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

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

PROCESS Translation {
    IS_A: GeneExpressionProcess
    INPUT: mRNA
    READS: CodonSequence
    EXECUTED_BY: Ribosome
    USES: tRNA
    OUTPUT: Polypeptide
    DIRECTION_OF_mRNA_READING: "5-prime to 3-prime"
    DIRECTION_OF_POLYPEPTIDE_SYNTHESIS: "N-terminus to C-terminus"
}

ENTITY mRNA {
    IS_A: RNA
    CONTAINS: [CodingSequence, Codon]
    TEMPLATE_FOR: Translation
}

ENTITY Codon {
    IS_A: NucleotideTriplet
    PART_OF: mRNA
    SPECIFIES: [AminoAcid, TranslationSignal]
}

ENTITY tRNA {
    IS_A: RNA
    CONTAINS: Anticodon
    CARRIES: AminoAcid
    PARTICIPATES_IN: Translation
}

ENTITY Anticodon {
    PART_OF: tRNA
    RECOGNIZES: Codon
    INTERACTS_BY: ComplementaryBasePairing
}

ENTITY Ribosome {
    IS_A: RibonucleoproteinComplex
    BINDS: mRNA
    COORDINATES: tRNA
    CATALYSES: PeptideBondFormation
}

ENTITY Polypeptide {
    COMPOSED_OF: AminoAcid
    PRODUCED_BY: Translation
    MAY_FORM: FunctionalProtein
}

# ============================================================
# GENETIC CODE
# ============================================================

ENTITY GeneticCode {
    MAPS: Codon
    TO: [AminoAcid, TranslationSignal]
}

ENTITY StartCodon {
    SUBCLASS_OF: Codon
    INITIATES: Translation
}

ENTITY StopCodon {
    SUBCLASS_OF: Codon
    TERMINATES: Translation
}

RELATION AUG IS_STANDARD_START_CODON_OF Translation
RELATION AUG ENCODES Methionine
RELATION UAA SIGNALS TranslationTermination
RELATION UAG SIGNALS TranslationTermination
RELATION UGA SIGNALS TranslationTermination

RULE CodeContextRule {
    IF organism_or_organelle USES GeneticCodeVariant
    THEN CodonInterpretation MUST_USE GeneticCodeVariant
}

# ============================================================
# AMINOACYL-tRNA CHARGING
# ============================================================

PROCESS tRNACharging {
    INPUTS: [tRNA, AminoAcid, ATP]
    CATALYSED_BY: Aminoacyl_tRNA_Synthetase
    OUTPUT: Aminoacyl_tRNA
}

ENTITY Aminoacyl_tRNA_Synthetase {
    IS_A: Enzyme
    RECOGNIZES: [tRNA, AminoAcid]
    CHARGES: tRNA
    CONTRIBUTES_TO: TranslationFidelity
}

ENTITY Aminoacyl_tRNA {
    IS_A: Charged_tRNA
    CARRIES: AminoAcid
}

RULE ChargingRule {
    IF Aminoacyl_tRNA_Synthetase recognizes compatible_tRNA
       AND correct_AminoAcid IS_AVAILABLE
    THEN tRNACharging MAY_PRODUCE Aminoacyl_tRNA
}

# ============================================================
# RIBOSOME STRUCTURE
# ============================================================

ENTITY RibosomalSubunit {
    PART_OF: Ribosome
    MAY_BE: [SmallSubunit, LargeSubunit]
}

ENTITY SmallSubunit {
    PARTICIPATES_IN: mRNA_Decoding
}

ENTITY LargeSubunit {
    PARTICIPATES_IN: PeptideBondFormation
}

ENTITY RibosomalSite {
    MAY_BE: [A_Site, P_Site, E_Site]
    PART_OF: Ribosome
}

ENTITY A_Site {
    BINDS: IncomingAminoacyl_tRNA
}

ENTITY P_Site {
    HOLDS: Peptidyl_tRNA
}

ENTITY E_Site {
    ASSOCIATED_WITH: Deacylated_tRNA_Exit
}

# ============================================================
# TRANSLATION INITIATION
# ============================================================

PROCESS TranslationInitiation {
    SUBPROCESS_OF: Translation
    REQUIRES: [
        mRNA,
        RibosomalSubunits,
        Initiator_tRNA,
        InitiationFactors
    ]
    ESTABLISHES: ReadingFrame
}

ENTITY Initiator_tRNA {
    SUBCLASS_OF: tRNA
    RECOGNIZES: StartCodon
}

ENTITY InitiationFactor {
    IS_A: TranslationFactor
    PARTICIPATES_IN: TranslationInitiation
}

RULE InitiationRule {
    IF Ribosome IS_POSITIONED_AT valid_start_context
       AND Initiator_tRNA RECOGNIZES StartCodon
    THEN TranslationInitiation MAY_COMPLETE
    AND ReadingFrame := established
}

# ============================================================
# TRANSLATION ELONGATION
# ============================================================

PROCESS TranslationElongation {
    SUBPROCESS_OF: Translation
    ITERATES_OVER: CodonSequence
    EXTENDS: Polypeptide
}

ENTITY ElongationFactor {
    IS_A: TranslationFactor
    PARTICIPATES_IN: TranslationElongation
}

PROCESS CodonRecognition {
    INPUTS: [Codon, Aminoacyl_tRNA]
    VALIDATES: CodonAnticodonPairing
}

PROCESS PeptideBondFormation {
    JOINS: AminoAcid
    TO: GrowingPolypeptide
    CATALYTIC_CENTER: Ribosome
}

PROCESS Translocation {
    MOVES: Ribosome
    ALONG: mRNA
    ADVANCE: OneCodon
}

RULE ElongationCycle {
    CodonRecognition
        -> PeptideBondFormation
        -> Translocation
        -> NextCodon
}

RULE CodonAdditionRule {
    IF correct_Aminoacyl_tRNA OCCUPIES A_Site
       AND PeptideBondFormation OCCURS
    THEN Polypeptide.length := Polypeptide.length + 1
}

# ============================================================
# TRANSLATION TERMINATION
# ============================================================

PROCESS TranslationTermination {
    SUBPROCESS_OF: Translation
    TRIGGERED_BY: StopCodon
    USES: ReleaseFactor
    RELEASES: Polypeptide
}

ENTITY ReleaseFactor {
    IS_A: TranslationFactor
    RECOGNIZES: StopCodon
    PROMOTES: PolypeptideRelease
}

RULE TerminationRule {
    IF StopCodon ENTERS ribosomal_A_Site
       AND compatible_ReleaseFactor BINDS
    THEN {
        RELEASE Polypeptide
        TERMINATE Translation
        RECYCLE ribosomal_components
    }
}

# ============================================================
# READING FRAME
# ============================================================

ENTITY ReadingFrame {
    DEFINES: CodonPartition
    OVER: CodingSequence
}

ENTITY OpenReadingFrame {
    IS_A: ReadingFrame
    MAY_BEGIN_WITH: StartCodon
    MAY_END_WITH: StopCodon
    MAY_ENCODE: Polypeptide
}

RULE FrameRule {
    IF TranslationInitiation position CHANGES
    THEN CodonPartition MAY_CHANGE
    AND PolypeptideSequence MAY_CHANGE
}

RULE FrameshiftRule {
    IF coding_insertion_or_deletion LENGTH mod 3 != 0
    THEN downstream_ReadingFrame MAY_SHIFT
}

# ============================================================
# POLYSOMES
# ============================================================

ENTITY Polysome {
    COMPOSED_OF: MultipleRibosomes
    TRANSLATING: Same_mRNA
}

RULE PolysomeRule {
    IF multiple_Ribosomes TRANSLATE same_mRNA simultaneously
    THEN Polysome EXISTS
}

# ============================================================
# PROKARYOTIC TRANSLATION
# ============================================================

PROCESS ProkaryoticTranslation {
    SUBCLASS_OF: Translation
    OCCURS_IN: ProkaryoticCell
    MAY_BE_COUPLED_WITH: Transcription
}

ENTITY RibosomeBindingSite {
    PART_OF: Prokaryotic_mRNA
    SUPPORTS: TranslationInitiation
}

RULE CoupledExpressionRule {
    IF organism == Prokaryote
       AND nascent_mRNA IS_ACCESSIBLE
    THEN Translation MAY_BEGIN_BEFORE TranscriptionTerminates
}

# ============================================================
# EUKARYOTIC TRANSLATION
# ============================================================

PROCESS EukaryoticTranslation {
    SUBCLASS_OF: Translation
    OCCURS_IN: EukaryoticCell
    MAY_DEPEND_ON: [
        FivePrimeCap,
        PolyATail,
        InitiationFactors,
        KozakContext
    ]
}

ENTITY KozakContext {
    SURROUNDS: StartCodon
    MAY_AFFECT: InitiationEfficiency
}

RULE EukaryoticInitiationContext {
    IF StartCodon EXISTS_IN favorable_KozakContext
    THEN initiation_probability MAY_INCREASE
}

# ============================================================
# TRANSLATIONAL REGULATION
# ============================================================

PROCESS TranslationalRegulation {
    TARGET: TranslationRateOrEfficiency
    MAY_ACT_AT: [
        Initiation,
        Elongation,
        Termination,
        mRNA_Availability,
        RibosomeRecruitment
    ]
}

ENTITY RegulatoryRNA {
    MAY_MODULATE: Translation
}

ENTITY RNA_BindingProtein {
    BINDS: RNA
    MAY_MODULATE: Translation
}

RULE TranslationalControlRule {
    IF RegulatoryFactor alters_ribosome_access_or_activity
    THEN TranslationEfficiency MAY_CHANGE
}

# ============================================================
# TRANSLATION FIDELITY
# ============================================================

ENTITY TranslationError {
    OCCURS_DURING: Translation
    MAY_CAUSE: IncorrectAminoAcidIncorporation
}

PROCESS Proofreading {
    CONTRIBUTES_TO: TranslationFidelity
    MAY_OCCUR_DURING: [
        tRNACharging,
        CodonRecognition
    ]
}

RULE FidelityRule {
    IF CodonAnticodonPairing IS_INCORRECT
       AND proofreading FAILS
    THEN TranslationError MAY_OCCUR
}

# ============================================================
# POST-TRANSLATIONAL RELATIONSHIP
# ============================================================

PROCESS ProteinFolding {
    INPUT: Polypeptide
    OUTPUT: FoldedProtein
}

PROCESS PostTranslationalModification {
    TARGET: ProteinOrPolypeptide
    MAY_CHANGE: [
        activity,
        stability,
        localization,
        interactions
    ]
}

RULE ProcessBoundary {
    Translation PRODUCES Polypeptide
    ProteinFolding != Translation
    PostTranslationalModification != Translation
}

# ============================================================
# TRANSLATION INHIBITION
# ============================================================

ENTITY TranslationInhibitor {
    REDUCES_OR_BLOCKS: Translation
    MAY_TARGET: [
        Ribosome,
        TranslationFactor,
        tRNACharging,
        mRNA
    ]
}

RULE InhibitionRule {
    IF TranslationInhibitor disrupts_required_translation_component
    THEN TranslationRate MAY_DECREASE
}

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

ENTITY TranslationFunction {
    DIMENSIONS: [
        GeneticInformationDecoding,
        PolypeptideSynthesis,
        GeneExpression,
        ProteomeGeneration
    ]
}

RELATION Translation DECODES mRNA
RELATION Translation USES GeneticCode
RELATION Translation PRODUCES Polypeptide
RELATION Translation PART_OF GeneExpression

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

ENTITY Evidence {
    TYPES: [
        BiochemicalEvidence,
        RibosomeProfilingEvidence,
        ProteomicEvidence,
        GeneticEvidence,
        StructuralEvidence,
        ComputationalEvidence,
        LiteratureEvidence
    ]
}

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

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

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

RELATION mRNA TEMPLATE_FOR Translation
RELATION Ribosome EXECUTES Translation
RELATION Codon RECOGNIZED_BY Anticodon
RELATION tRNA CARRIES AminoAcid
RELATION GeneticCode MAPS Codon TO AminoAcid
RELATION Translation PRODUCES Polypeptide
RELATION Polypeptide MAY_FORM Protein
RELATION Translation PART_OF GeneExpression

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

SEMANTIC_EQUIVALENCE {
    "translation" ~= "protein synthesis from mRNA template" WHEN context == gene_expression
    "protein synthesis" ~= "translation" WHEN referring_to_ribosomal_polypeptide_synthesis
    "charged tRNA" ~= "aminoacyl-tRNA"
    "termination codon" ~= "stop codon"
    "initiation codon" ~= "start codon"
}

RULE EquivalenceConstraint {
    IF terms ARE semantic_equivalents
    THEN preserve_mRNA_context()
    AND preserve_reading_frame()
    AND preserve_genetic_code_context()
    AND preserve_organism_context()
    AND prevent_false_identity()
}

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

CONFIDENCE TranslationAssertion {
    INPUTS: [
        biochemical_support,
        ribosome_profiling_support,
        proteomic_support,
        structural_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 SequenceTranslationInference {
    IF mRNA HAS valid_CodingSequence
       AND ReadingFrame IS_DEFINED
       AND GeneticCode IS_KNOWN
    THEN Polypeptide.sequence := translate(
        mRNA.CodingSequence,
        ReadingFrame,
        GeneticCode
    )
}

RULE CodonAminoAcidInference {
    IF Codon VALUE == codon_x
       AND GeneticCode MAPS codon_x TO AminoAcid_y
    THEN Translation MAY_ADD AminoAcid_y
}

RULE GeneProductInference {
    IF Gene TRANSCRIBED_TO mRNA
       AND mRNA TRANSLATED_TO Polypeptide
    THEN Polypeptide IS_GENE_PRODUCT_OF Gene
}

RULE StopInference {
    IF Ribosome ENCOUNTERS StopCodon
    THEN TranslationTermination SHOULD_OCCUR
    subject_to_context()
}

RULE VariantTranslationInference {
    IF CodingVariant CHANGES CodonSequence
    THEN PolypeptideEffect := compare_translation(
        reference_sequence,
        altered_sequence,
        reading_frame,
        genetic_code
    )
}

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

QUERY TranslationLookup(transcript_identifier) {
    RETURN [
        mRNA_identity,
        coding_sequence,
        reading_frame,
        start_codon,
        stop_codon,
        codon_sequence,
        genetic_code,
        predicted_or_observed_polypeptide,
        ribosome_evidence,
        regulatory_context,
        evidence,
        confidence
    ]
}

QUERY CodonTranslationLookup(codon, genetic_code_context) {
    RETURN [
        codon,
        amino_acid_or_signal,
        compatible_tRNAs,
        code_variant,
        evidence,
        confidence
    ]
}

QUERY TranslationVariantLookup(reference_sequence, altered_sequence) {
    RETURN [
        affected_codons,
        reading_frame_effect,
        amino_acid_changes,
        premature_stop,
        stop_loss,
        predicted_polypeptide_change,
        evidence,
        confidence
    ]
}

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

UPDATE_MODEL {
    ON new_translation_evidence:
        validate_provenance()
        identify_organism()
        normalize_transcript_identifier()
        normalize_protein_identifier()
        establish_reading_frame()
        identify_genetic_code_variant()
        map_codons_and_translation_signals()
        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: [
        transcript_identity,
        coding_sequence,
        reading_frame,
        genetic_code_context,
        codon_mapping,
        ribosome_context,
        polypeptide_identity,
        evidence_provenance,
        confidence,
        semantic_equivalence
    ]

    REQUIREMENTS: [
        distinguish_translation_from_transcription,
        distinguish_mRNA_from_polypeptide,
        distinguish_codon_from_anticodon,
        preserve_sequence_direction,
        preserve_reading_frame,
        preserve_species_context,
        preserve_organelle_context,
        use_correct_genetic_code_variant,
        distinguish_observed_from_predicted_translation,
        avoid_unsupported_causal_inference
    ]
}

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

VALIDATE {
    REQUIRE Translation
    REQUIRE mRNA
    REQUIRE Codon
    REQUIRE tRNA
    REQUIRE Anticodon
    REQUIRE Ribosome
    REQUIRE TranslationInitiation
    REQUIRE TranslationElongation
    REQUIRE TranslationTermination
    REQUIRE Evidence
    REQUIRE CONFIDENCE
    REQUIRE SEMANTIC_EQUIVALENCE
    REQUIRE UPDATE_MODEL
    REQUIRE AI_CONSUMPTION

    ASSERT Translation INPUT == mRNA
    ASSERT Translation OUTPUT == Polypeptide
    ASSERT Ribosome EXECUTES Translation
    ASSERT Codon != Anticodon
    ASSERT Translation != Transcription
    ASSERT Translation != ProteinFolding
}

# ============================================================
# 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 "TranslationOntology"