Ribosome Ontology

AI SEARCH FLOW ALGEBRA
RIBOSOME ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

SOURCE
https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/cell-biology/ribosome-ontology.html

FLOW "RibosomeOntology" v4.0
DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / RIBOSOME
ONTOLOGY := RIBOSOME_ONTOLOGY

RIBOSOME := RIBOSOME_IDENTITY + SMALL_SUBUNIT + LARGE_SUBUNIT + RIBOSOMAL_RNA + RIBOSOMAL_PROTEINS + RIBOSOME_BIOGENESIS + SUBUNIT_ASSEMBLY + MRNA_BINDING + TRNA_BINDING + CODON_DECODING + TRANSLATION_INITIATION + ELONGATION + TERMINATION + PEPTIDE_BOND_FORMATION + TRANSLOCATION + TRANSLATIONAL_FIDELITY + POLYRIBOSOMES + CELLULAR_LOCALISATION + TRANSLATIONAL_REGULATION + QUALITY_CONTROL + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE := IDENTIFY_RIBOSOME -> CLASSIFY_RIBOSOME_CONTEXT -> MAP_SMALL_AND_LARGE_SUBUNITS -> MAP_RRNA_AND_RIBOSOMAL_PROTEINS -> MAP_BIOGENESIS_AND_ASSEMBLY -> MAP_MRNA_AND_TRNA_INTERACTIONS -> MAP_INITIATION_ELONGATION_AND_TERMINATION -> MAP_DECODING_AND_PEPTIDE_BOND_FORMATION -> MAP_TRANSLOCATION_AND_FIDELITY -> MAP_CELLULAR_LOCALISATION_AND_TARGETING -> MAP_REGULATION_AND_QUALITY_CONTROL -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY Ribosome
ENTITY SmallSubunit
ENTITY LargeSubunit
ENTITY RibosomalRNA
ENTITY RibosomalProtein
ENTITY MessengerRNA
ENTITY TransferRNA
ENTITY Codon
ENTITY Anticodon
ENTITY AminoAcid
ENTITY AminoacylTRNA
ENTITY Polypeptide
ENTITY Translation
ENTITY TranslationInitiation
ENTITY TranslationElongation
ENTITY TranslationTermination
ENTITY RibosomeBiogenesis
ENTITY DecodingCenter
ENTITY PeptidylTransferaseCenter
ENTITY ASite
ENTITY PSite
ENTITY ESite
ENTITY TranslationFactor
ENTITY Polyribosome
ENTITY TranslationalFidelity
ENTITY RibosomeQualityControl
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# STRUCTURE / BIOGENESIS
Ribosome -> ribonucleoprotein_complex_that -> PERFORMS_TRANSLATION
Ribosome -> composed_of -> SmallSubunit + LargeSubunit
RIBOSOME_CONTEXT := PROKARYOTIC_CYTOSOLIC | EUKARYOTIC_CYTOSOLIC | MITOCHONDRIAL | CHLOROPLAST | OTHER_ORGANELLE_SPECIFIC_AS_APPLICABLE
SmallSubunit -> primarily_supports -> MRNA_BINDING + CODON_DECODING
LargeSubunit -> primarily_supports -> PEPTIDE_BOND_FORMATION + NASCENT_POLYPEPTIDE_EXIT
RibosomalSubunit -> composed_of -> RibosomalRNA + RibosomalProtein
RibosomalRNA -> structural_and_catalytic_component_of -> Ribosome
RibosomalProtein -> contributes_to -> ASSEMBLY + STRUCTURAL_STABILITY + RRNA_INTERACTION + TRANSLATIONAL_FUNCTION

RibosomeBiogenesis -> produces -> MATURE_RIBOSOMAL_SUBUNITS
BIOGENESIS_FLOW := RRNA_TRANSCRIPTION -> RRNA_PROCESSING -> RRNA_MODIFICATION -> RIBOSOMAL_PROTEIN_ASSOCIATION -> SUBUNIT_ASSEMBLY -> MATURATION -> CELLULAR_LOCALISATION
RibosomeBiogenesis -> requires -> RRNA + RIBOSOMAL_PROTEINS + ASSEMBLY_FACTORS + ENERGY
InEukaryotes: Nucleolus -> major_site_of -> MANY_RIBOSOME_BIOGENESIS_STEPS

# MRNA / TRNA / TRANSLATION
MessengerRNA -> provides -> CODON_SEQUENCE -> for -> TRANSLATION
Ribosome -> binds -> MessengerRNA
Codon -> specifies -> AMINO_ACID_OR_TRANSLATION_SIGNAL -> according_to -> GENETIC_CODE
TransferRNA -> carries -> AminoAcid -> to -> Ribosome
TransferRNA -> contains -> Anticodon
Anticodon -> base_pairs_with -> Codon
AminoacylTRNA -> charged_form_of -> TransferRNA

ASite -> binds -> INCOMING_AMINOACYL_TRNA
PSite -> holds -> PEPTIDYL_TRNA_AS_DEFINED
ESite -> associated_with -> DEACYLATED_TRNA_EXIT
Ribosome -> contains_functional_sites -> ASite + PSite + ESite

Translation -> converts -> MRNA_CODON_INFORMATION -> into -> POLYPEPTIDE_SEQUENCE
TRANSLATION_FLOW := INITIATION -> ELONGATION -> TERMINATION -> RIBOSOME_RECYCLING
Translation -> requires -> MRNA + RIBOSOME + TRNAS + AMINO_ACIDS + TRANSLATION_FACTORS + ENERGY

# INITIATION / ELONGATION / DECODING / TERMINATION
TranslationInitiation -> establishes -> CORRECT_START_SITE + INITIATOR_TRNA_POSITION + ASSEMBLED_TRANSLATION_COMPLEX
INITIATION_FLOW := SMALL_SUBUNIT_RECRUITMENT -> MRNA_RECOGNITION -> START_CODON_SELECTION -> INITIATOR_TRNA_PLACEMENT -> LARGE_SUBUNIT_JOINING
StartCodonRecognition -> establishes -> TRANSLATIONAL_READING_FRAME

TranslationElongation -> extends -> NASCENT_POLYPEPTIDE
ELONGATION_CYCLE := AMINOACYL_TRNA_DELIVERY -> CODON_RECOGNITION -> ACCOMMODATION -> PEPTIDE_BOND_FORMATION -> TRANSLOCATION

DecodingCenter -> evaluates -> CODON_ANTICODON_INTERACTION
CodonAnticodonPairing -> determines -> TRNA_ACCEPTANCE_OR_REJECTION
Decoding -> contributes_to -> AMINO_ACID_SEQUENCE_ACCURACY

PeptidylTransferaseCenter -> catalyses -> PEPTIDE_BOND_FORMATION
RibosomalRNA -> contributes_directly_to -> PEPTIDYL_TRANSFERASE_CATALYSIS
Translocation -> advances -> RIBOSOME -> by -> ONE_CODON_STEP_AS_DEFINED

TranslationTermination -> occurs_when -> STOP_CODON -> enters -> DECODING_POSITION_AS_DEFINED
Termination -> releases -> COMPLETED_POLYPEPTIDE
TERMINATION_FLOW := STOP_CODON_RECOGNITION -> PEPTIDYL_TRNA_HYDROLYSIS -> POLYPEPTIDE_RELEASE -> RIBOSOME_RECYCLING

# FIDELITY / LOCALISATION / REGULATION
TranslationalFidelity -> represents -> ACCURACY_OF_INFORMATION_TRANSFER -> from -> MRNA -> to -> POLYPEPTIDE
FIDELITY_COMPONENT := START_SITE_SELECTION | CODON_DECODING | TRNA_SELECTION | READING_FRAME_MAINTENANCE | TERMINATION_ACCURACY
Fidelity -> depends_on -> RIBOSOME + TRNA_CHARGING + TRANSLATION_FACTORS + MRNA_CONTEXT + CELLULAR_CONDITIONS
IF NearCognateTRNA incorrectly_accepted THEN TranslationError -> MAY_OCCUR

Polyribosome -> consists_of -> MULTIPLE_RIBOSOMES -> translating -> SAME_MRNA
Polyribosome -> increases -> PARALLEL_TRANSLATIONAL_OUTPUT_FROM_MRNA

Ribosome -> may_transition_between -> FREE + MEMBRANE_ASSOCIATED_STATES
ERAssociatedRibosome -> associated_with -> ROUGH_ENDOPLASMIC_RETICULUM
CoTranslationalTranslocation -> moves -> NASCENT_POLYPEPTIDE -> into_or_across -> ER_MEMBRANE
MitochondrialRibosome -> translates -> MITOCHONDRIAL_GENOME_ENCODED_MRNA_AS_APPLICABLE
ChloroplastRibosome -> translates -> CHLOROPLAST_GENOME_ENCODED_MRNA_AS_APPLICABLE

TranslationalRegulation -> changes -> PROTEIN_SYNTHESIS_RATE -> without_necessarily_changing -> MRNA_ABUNDANCE
REGULATION_TARGET := INITIATION | ELONGATION | TERMINATION | RIBOSOME_AVAILABILITY | MRNA_ACCESSIBILITY
IF InitiationRate changes THEN ProteinOutput -> MAY_CHANGE

# STALLING / QUALITY CONTROL / EVIDENCE
RibosomeStalling -> represents -> PAUSE_OR_ARREST_OF_TRANSLATION
STALL_CAUSE := DAMAGED_MRNA | DIFFICULT_SEQUENCE | TRNA_LIMITATION | AMINO_ACID_LIMITATION | NASCENT_CHAIN_INTERACTION | DRUG_OR_TOXIN | OTHER_TRANSLATIONAL_OBSTACLE
StalledRibosome -> may_activate -> RIBOSOME_RESCUE + QUALITY_CONTROL
RibosomeRescue -> releases_or_recovers -> STALLED_TRANSLATION_COMPLEX
RibosomeRescue -> restores -> TRANSLATIONAL_CAPACITY

RibosomeQualityControl -> detects_or_manages -> ABERRANT_TRANSLATION + STALLED_RIBOSOMES + DEFECTIVE_RIBOSOMAL_COMPONENTS
QUALITY_CONTROL_TARGET := MRNA | NASCENT_POLYPEPTIDE | RIBOSOME | RIBOSOMAL_SUBUNIT
QualityControl -> may_trigger -> MRNA_DECAY + NASCENT_CHAIN_DEGRADATION + RIBOSOME_RECYCLING + RIBOSOME_REPAIR_OR_TURNOVER

RibosomeClaim -> supported_by -> Evidence
EVIDENCE_TYPE := STRUCTURAL | BIOCHEMICAL | MOLECULAR | GENETIC | RIBOSOME_PROFILING | CRYO_EM | FUNCTIONAL | PERTURBATION | COMPUTATIONAL
Evidence -> has -> SOURCE + METHOD + CELL_OR_SAMPLE + RIBOSOME_CONTEXT + CONDITION + QUALITY + UNCERTAINTY
RIBOSOME_UNCERTAINTY := MEASUREMENT_UNCERTAINTY + STRUCTURAL_STATE_UNCERTAINTY + TRANSLATION_STATE_UNCERTAINTY + CELL_TO_CELL_VARIABILITY + MODEL_UNCERTAINTY
Uncertainty -> qualifies -> RibosomeClaim + TranslationRate + RibosomeState + FidelityEstimate

Provenance -> records -> RIBOSOME_IDENTITY + CELLULAR_CONTEXT + SUBUNIT_STATE + MRNA + TRANSLATION_STATE + METHOD + CONDITION + MEASUREMENT + TIME + VERSION
Ribosome -> linked_to -> Provenance

# REASONING / INFERENCE
RIBOSOME_REASONING := IDENTIFY_RIBOSOME -> CLASSIFY_CONTEXT -> MAP_SUBUNITS -> MAP_RRNA_AND_RIBOSOMAL_PROTEINS -> MAP_BIOGENESIS -> MAP_MRNA_AND_TRNA_INTERACTIONS -> MAP_INITIATION -> MAP_ELONGATION -> MAP_DECODING -> MAP_PEPTIDE_BOND_FORMATION -> MAP_TRANSLOCATION -> MAP_TERMINATION_AND_RECYCLING -> MAP_FIDELITY -> MAP_CELLULAR_LOCALISATION -> MAP_TRANSLATIONAL_REGULATION -> MAP_STALLING_RESCUE_AND_QUALITY_CONTROL -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

IF RibosomeAssembly fails THEN TranslationCapacity -> MAY_DECREASE
IF StartSiteSelection changes THEN ReadingFrameOrProteinOutput -> MAY_CHANGE
IF TRNASelectionAccuracy decreases THEN TranslationErrorRate -> MAY_INCREASE
IF Translocation fails THEN TranslationElongation -> MAY_STALL
IF RibosomeStalling increases THEN QualityControlActivation -> MAY_INCREASE
IF CellularEnergyState decreases THEN TranslationRate -> MAY_DECREASE
IF RibosomeLocalization changes THEN ProteinTargetingContext -> MAY_CHANGE
IF Evidence insufficient THEN RibosomeClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION composed_of(Ribosome, SmallSubunit)
RELATION composed_of(Ribosome, LargeSubunit)
RELATION component_of(RibosomalRNA, Ribosome)
RELATION component_of(RibosomalProtein, Ribosome)
RELATION binds(Ribosome, MessengerRNA)
RELATION carries(TransferRNA, AminoAcid)
RELATION base_pairs_with(Anticodon, Codon)
RELATION binds(ASite, AminoacylTRNA)
RELATION catalyses(PeptidylTransferaseCenter, PeptideBondFormation)
RELATION evaluates(DecodingCenter, CodonAnticodonInteraction)
RELATION extends(TranslationElongation, Polypeptide)
RELATION releases(TranslationTermination, Polypeptide)
RELATION consists_of(Polyribosome, Ribosome)
RELATION regulates(TranslationalRegulation, ProteinSynthesis)
RELATION manages(RibosomeQualityControl, AberrantTranslation)
RELATION supports(Evidence, RibosomeClaim)
RELATION records(Provenance, Ribosome)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "ribosome" ~= "ribonucleoprotein complex that translates messenger RNA into polypeptide"
  "small ribosomal subunit" ~= "ribosomal subunit principally associated with mRNA decoding"
  "large ribosomal subunit" ~= "ribosomal subunit principally associated with peptide-bond formation"
  "decoding center" ~= "ribosomal region evaluating codon-anticodon interactions"
  "peptidyl transferase center" ~= "ribosomal catalytic center for peptide-bond formation"
  "translation initiation" ~= "assembly and start-site establishment of a translation complex"
  "translation elongation" ~= "cyclic extension of a nascent polypeptide"
  "translation termination" ~= "stop-signal-dependent release of a completed polypeptide"
  "polyribosome" ~= "multiple ribosomes translating the same messenger RNA"
  "ribosome quality control" ~= "cellular surveillance and management of defective translation complexes"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  ribosome_structure_mapping: 0.99
  biogenesis_mapping: 0.99
  mrna_trna_mapping: 0.99
  initiation_elongation_mapping: 0.99
  decoding_catalysis_mapping: 0.99
  termination_recycling_mapping: 0.99
  localisation_regulation_mapping: 0.99
  quality_control_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_ribosome_observation:
    MAP ribosome_context
    MAP subunit_state
    MAP rRNA_and_protein_composition
    MAP translation_state
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON translation_event:
    UPDATE mrna_state
    UPDATE trna_state
    UPDATE nascent_chain_state
    UPDATE ribosome_position
    PRESERVE provenance
  ON ribosome_stall:
    UPDATE stall_state
    UPDATE rescue_state
    UPDATE quality_control_state
    PRESERVE provenance
  ON new_structural_or_functional_evidence:
    UPDATE ribosome_model
    UPDATE evidence_quality
    UPDATE uncertainty
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_RIBOSOME_ONTOLOGY
  reasoning_mode: TRANSLATIONAL_RIBONUCLEOPROTEIN_RELATIONAL
  preserve: [typed_entities, ribosome_identity, ribosome_context, subunit_state, rRNA_state, ribosomal_protein_state, mrna_state, trna_state, translation_stage, ribosome_position, fidelity_state, localisation, regulation_state, quality_control_state, evidence, uncertainty, confidence, provenance]
  infer: [assembly_dependencies, decoding_dependencies, elongation_state, termination_state, translational_fidelity, localisation_effects, regulation_effects, stall_and_rescue_state, evidence_strength]
  prohibit: [invented_translation_observations, fabricated_ribosome_composition, unsupported_codon_assignment, assumed_translation_rate_without_evidence, unsupported_stall_mechanism, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + STRUCTURE_BIOGENESIS + MRNA_TRNA_TRANSLATION + INITIATION_ELONGATION_DECODING_TERMINATION + FIDELITY_LOCALISATION_REGULATION + STALLING_QUALITY_CONTROL_EVIDENCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW