RNA Ontology

AI SEARCH FLOW ALGEBRA
RNA ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

SOURCE
https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/molecular-biology/rna-ontology.html

FLOW "RNAOntology" v4.0
DOMAIN := BIOLOGICAL_ONTOLOGIES / MOLECULAR_BIOLOGY / RNA
ONTOLOGY := RNA_ONTOLOGY

RNA := RNA_IDENTITY + RIBONUCLEOTIDES + RNA_STRAND + RNA_SEQUENCE + RNA_STRUCTURE + MRNA + TRNA + RRNA + NONCODING_RNA + TRANSCRIPTION + RNA_PROCESSING + SPLICING + RNA_EDITING + RNA_MODIFICATION + RNA_LOCALISATION + RNA_PROTEIN_INTERACTIONS + RNA_RNA_INTERACTIONS + TRANSLATION_ROLE + RNA_REGULATION + RNA_TURNOVER + RNA_QUALITY_CONTROL + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE := IDENTIFY_RNA -> MAP_NUCLEOTIDE_SEQUENCE_AND_STRUCTURE -> CLASSIFY_RNA_TYPE -> MAP_TRANSCRIPTION_AND_PROCESSING -> MAP_SPLICING_EDITING_AND_MODIFICATION -> MAP_RNA_INTERACTIONS_AND_LOCALISATION -> MAP_TRANSLATIONAL_AND_REGULATORY_ROLES -> MAP_TURNOVER_AND_QUALITY_CONTROL -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY RNA
ENTITY Ribonucleotide
ENTITY Ribose
ENTITY Phosphate
ENTITY Adenine
ENTITY Uracil
ENTITY Guanine
ENTITY Cytosine
ENTITY RNAStrand
ENTITY RNASequence
ENTITY RNASecondaryStructure
ENTITY RNATertiaryStructure
ENTITY MessengerRNA
ENTITY TransferRNA
ENTITY RibosomalRNA
ENTITY NoncodingRNA
ENTITY MicroRNA
ENTITY SmallInterferingRNA
ENTITY LongNoncodingRNA
ENTITY SmallNuclearRNA
ENTITY SmallNucleolarRNA
ENTITY Transcription
ENTITY RNApolymerase
ENTITY RNAProcessing
ENTITY Splicing
ENTITY Intron
ENTITY Exon
ENTITY RNAEditing
ENTITY RNAModification
ENTITY RNABindingProtein
ENTITY Ribosome
ENTITY Codon
ENTITY Anticodon
ENTITY RNALocalisation
ENTITY RNATurnover
ENTITY RNAQualityControl
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# RNA IDENTITY / STRUCTURE
RNA -> biomolecule_type -> NUCLEIC_ACID
RNA -> polymer_of -> Ribonucleotide
Ribonucleotide -> composed_of -> RIBOSE + PHOSPHATE + NITROGENOUS_BASE
RNA_BASE := ADENINE | URACIL | GUANINE | CYTOSINE
RNAStrand -> has_directionality -> FIVE_PRIME_TO_THREE_PRIME
RNASequence -> ordered_arrangement_of -> RNA_BASES
RNAIdentity -> depends_on -> SEQUENCE + STRUCTURE + MODIFICATION + BINDING_PARTNERS + LOCALISATION + BIOLOGICAL_CONTEXT

RNASecondaryStructure -> may_include -> STEM + LOOP + HAIRPIN + BULGE + INTERNAL_LOOP + PSEUDOKNOT_AS_APPLICABLE
RNATertiaryStructure -> emerges_from -> LONG_RANGE_INTRAMOLECULAR_INTERACTIONS
RNAStructure -> influences -> STABILITY + INTERACTION + CATALYSIS + LOCALISATION + FUNCTION

# RNA TYPES
RNA_TYPE := MRNA | TRNA | RRNA | MICRORNA | SIRNA | LONG_NONCODING_RNA | SNRNA | SNORNA | OTHER_REGULATORY_RNA | OTHER_STRUCTURAL_RNA | OTHER_CATALYTIC_RNA
MessengerRNA -> carries -> CODING_INFORMATION_FOR_TRANSLATION
TransferRNA -> couples -> CODON_RECOGNITION + AMINO_ACID_DELIVERY
RibosomalRNA -> structural_and_catalytic_component_of -> RIBOSOME
NoncodingRNA -> functions_without_required_translation_to_protein -> TRUE
RNAFunction -> depends_on -> RNA_TYPE + SEQUENCE + STRUCTURE + LOCALISATION + INTERACTIONS

# TRANSCRIPTION
Transcription -> synthesises -> RNA -> from -> DNA_TEMPLATE
RNApolymerase -> catalyses -> RNA_SYNTHESIS
TRANSCRIPTION_FLOW := PROMOTER_OR_REGULATORY_RECOGNITION -> INITIATION -> ELONGATION -> TERMINATION -> PRIMARY_RNA_PRODUCT
PrimaryTranscript -> may_require -> RNA_PROCESSING
TranscriptionRate -> influenced_by -> REGULATORY_DNA + TRANSCRIPTION_FACTORS + CHROMATIN_STATE + SIGNALING

# RNA PROCESSING / SPLICING
RNAProcessing -> converts_or_modifies -> PRIMARY_OR_PRECURSOR_RNA
RNA_PROCESSING_TYPE := FIVE_PRIME_CAPPING_AS_APPLICABLE | SPLICING | THREE_PRIME_CLEAVAGE | POLYADENYLATION_AS_APPLICABLE | RNA_EDITING | RNA_MODIFICATION | PROCESSING_CLEAVAGE | RNA_QUALITY_CONTROL
Splicing -> removes -> INTRONS_AS_APPLICABLE
Splicing -> joins -> EXONS
AlternativeSplicing -> may_generate -> MULTIPLE_RNA_ISOFORMS
SpliceSiteSelection -> depends_on -> RNA_SEQUENCE + SPLICING_FACTORS + REGULATORY_ELEMENTS + CELLULAR_CONTEXT
IF SpliceSiteSelection changes THEN RNAIsoformOutput -> MAY_CHANGE

# RNA EDITING / MODIFICATION
RNAEditing -> changes -> RNA_SEQUENCE_INFORMATION_AFTER_TRANSCRIPTION_AS_DEFINED
RNAEditingEffect -> may_change -> CODING_INFORMATION + RNA_STRUCTURE + STABILITY + INTERACTION
RNAModification -> chemically_modifies -> RNA
RNAModification -> may_influence -> RNA_FOLDING + STABILITY + TRANSLATION + RECOGNITION + LOCALISATION
ModificationEffect -> depends_on -> RNA_TYPE + MODIFICATION_SITE + CELLULAR_CONTEXT

# MRNA / TRANSLATION
MessengerRNA -> contains -> CODONS
Codon -> specifies -> AMINO_ACID_OR_TRANSLATION_SIGNAL -> according_to -> GENETIC_CODE
Ribosome -> binds -> MessengerRNA
Translation -> reads -> MRNA_CODON_SEQUENCE
TRANSLATIONAL_RNA_FLOW := MRNA_RECRUITMENT -> START_SITE_SELECTION -> CODON_DECODING -> ELONGATION -> STOP_CODON_RECOGNITION -> RIBOSOME_RECYCLING
MRNAStructure -> influences -> TRANSLATION_INITIATION + ELONGATION + REGULATION
MRNAStability -> influences -> PROTEIN_OUTPUT

# TRNA
TransferRNA -> contains -> Anticodon
Anticodon -> base_pairs_with -> Codon
TransferRNA -> charged_with -> AMINO_ACID_AS_APPLICABLE
AminoacylTRNA -> delivers -> AMINO_ACID -> to -> RIBOSOME
TRNAIdentity -> recognised_by -> AMINOACYL_TRNA_SYNTHETASE_AS_DEFINED
TRNAModification -> may_influence -> FOLDING + DECODING + STABILITY

# RRNA
RibosomalRNA -> combines_with -> RIBOSOMAL_PROTEINS
RibosomalRNA -> contributes_to -> RIBOSOME_STRUCTURE + CODON_DECODING + PEPTIDE_BOND_FORMATION
RRNAProcessing -> produces -> MATURE_RRNA_SPECIES
RRNAModification -> may_support -> RIBOSOME_ASSEMBLY + FUNCTION
RibosomeBiogenesis -> requires -> RRNA_SYNTHESIS + PROCESSING + MODIFICATION + RIBOSOMAL_PROTEIN_ASSEMBLY

# REGULATORY NON-CODING RNA
MicroRNA -> may_regulate -> TARGET_MRNA
SmallInterferingRNA -> may_direct -> SEQUENCE_SPECIFIC_RNA_SILENCING_AS_APPLICABLE
LongNoncodingRNA -> may_function_in -> TRANSCRIPTIONAL_REGULATION + CHROMATIN_REGULATION + MOLECULAR_SCAFFOLDING + RNA_PROCESSING + OTHER_CONTEXTUAL_FUNCTION
SmallNuclearRNA -> participates_in -> RNA_PROCESSING_AS_APPLICABLE
SmallNucleolarRNA -> participates_in -> RRNA_PROCESSING_OR_MODIFICATION_AS_APPLICABLE
RegulatoryRNAEffect -> depends_on -> TARGET + COMPLEX_PARTNERS + LOCALISATION + CELLULAR_CONTEXT

# RNA-PROTEIN / RNA-RNA INTERACTIONS
RNABindingProtein -> binds -> RNA
RNAProteinInteraction -> may_change -> RNA_PROCESSING + STABILITY + LOCALISATION + TRANSLATION + DEGRADATION
RNARNAInteraction -> connects -> RNA_A + RNA_B
RNAHybridisation -> depends_on -> COMPLEMENTARITY + STRUCTURE + ACCESSIBILITY + ENVIRONMENT
RibonucleoproteinComplex -> assembled_from -> RNA + PROTEIN

# RNA LOCALISATION / TRANSPORT
RNALocalisation -> determines -> SUBCELLULAR_POSITION_OF_RNA
RNATransport -> moves -> RNA -> between_or_within -> CELLULAR_COMPARTMENTS
RNAExport -> may_transport -> PROCESSED_RNA -> from -> NUCLEUS -> to -> CYTOPLASM
LocalisationSignal -> may_be_encoded_in -> RNA_SEQUENCE_OR_STRUCTURE
RNALocalisation -> influences -> TRANSLATION + REGULATION + LOCAL_FUNCTION

# RNA TURNOVER
RNATurnover -> controls -> RNA_ABUNDANCE
RNADegradation -> removes -> RNA
RNAHalfLife -> influences -> STEADY_STATE_RNA_LEVEL
RNAStability -> depends_on -> SEQUENCE + STRUCTURE + MODIFICATION + RNA_BINDING_PROTEINS + TRANSLATIONAL_STATE + CELLULAR_CONTEXT
IF RNADegradation increases THEN RNAAbundance -> MAY_DECREASE

# RNA QUALITY CONTROL
RNAQualityControl -> detects_or_manages -> ABERRANT_OR_DEFECTIVE_RNA
QUALITY_CONTROL_TARGET := MISPROCESSED_RNA | PREMATURE_TERMINATION_CONTEXT | STALLED_TRANSLATION_ASSOCIATED_RNA | DAMAGED_RNA | OTHER_ABERRANT_RNA
RNAQualityControl -> may_trigger -> RNA_DEGRADATION + TRANSLATION_REPRESSION + RIBOSOME_RESCUE_AS_APPLICABLE
QualityControl -> supports -> TRANSCRIPTOME_INTEGRITY

# EVIDENCE / UNCERTAINTY / PROVENANCE
RNAClaim -> supported_by -> Evidence
EVIDENCE_TYPE := RNA_SEQUENCING | DIRECT_RNA_SEQUENCING_AS_APPLICABLE | TRANSCRIPTOMIC | STRUCTURAL | BIOCHEMICAL | MOLECULAR | GENETIC | INTERACTION_ASSAY | LOCALISATION_IMAGING | TRANSLATION_ASSAY | FUNCTIONAL | COMPUTATIONAL
Evidence -> has -> SOURCE + METHOD + SAMPLE + RNA_IDENTITY + ISOFORM_AS_APPLICABLE + CELLULAR_CONTEXT + CONDITION + QUALITY + UNCERTAINTY
RNA_UNCERTAINTY := SEQUENCING_UNCERTAINTY + ISOFORM_ASSIGNMENT_UNCERTAINTY + STRUCTURE_UNCERTAINTY + MODIFICATION_UNCERTAINTY + LOCALISATION_UNCERTAINTY + EXPRESSION_VARIABILITY + MODEL_UNCERTAINTY
Uncertainty -> qualifies -> RNAClaim + RNAIdentity + IsoformAssignment + StructureState + FunctionalInterpretation
Provenance -> records -> SAMPLE_IDENTITY + RNA_IDENTITY + RNA_SEQUENCE_OR_REGION + ISOFORM + MODIFICATION_STATE + LOCALISATION + METHOD + CONDITION + ANALYSIS + TIME + VERSION
RNA -> linked_to -> Provenance

# REASONING
RNA_REASONING := IDENTIFY_RNA -> MAP_NUCLEOTIDE_SEQUENCE -> MAP_SECONDARY_AND_TERTIARY_STRUCTURE -> CLASSIFY_RNA_TYPE -> MAP_TRANSCRIPTION -> MAP_PROCESSING_AND_SPLICING -> MAP_EDITING_AND_MODIFICATION -> MAP_MRNA_TRANSLATION_ROLE -> MAP_TRNA_DECODING_ROLE -> MAP_RRNA_RIBOSOME_ROLE -> MAP_NONCODING_REGULATION -> MAP_RNA_PROTEIN_AND_RNA_RNA_INTERACTIONS -> MAP_LOCALISATION_AND_TRANSPORT -> MAP_TURNOVER -> MAP_QUALITY_CONTROL -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF RNASequence changes THEN RNAStructureOrFunction -> MAY_CHANGE
IF Splicing changes THEN RNAIsoformOutput -> MAY_CHANGE
IF RNAEditing changes THEN RNAInformationContent -> MAY_CHANGE
IF RNAModification changes THEN RNAStabilityOrFunction -> MAY_CHANGE
IF RNABindingProteinInteraction changes THEN RNAProcessingLocalisationOrTurnover -> MAY_CHANGE
IF MRNAStability decreases THEN ProteinOutput -> MAY_DECREASE
IF RegulatoryRNATargeting increases THEN TargetExpression -> MAY_CHANGE
IF RNAQualityControl fails THEN AberrantRNAAccumulation -> MAY_INCREASE
IF Evidence insufficient THEN RNAClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION polymer_of(RNA, Ribonucleotide)
RELATION synthesises(Transcription, RNA)
RELATION catalyses(RNApolymerase, RNASynthesis)
RELATION modifies(RNAProcessing, RNA)
RELATION removes(Splicing, Intron)
RELATION joins(Splicing, Exon)
RELATION modifies(RNAEditing, RNASequence)
RELATION modifies(RNAModification, RNA)
RELATION carries(MessengerRNA, CodingInformation)
RELATION contains(TransferRNA, Anticodon)
RELATION base_pairs_with(Anticodon, Codon)
RELATION component_of(RibosomalRNA, Ribosome)
RELATION regulates(MicroRNA, TargetRNA)
RELATION binds(RNABindingProtein, RNA)
RELATION moves(RNATransport, RNA)
RELATION removes(RNADegradation, RNA)
RELATION manages(RNAQualityControl, AberrantRNA)
RELATION supports(Evidence, RNAClaim)
RELATION records(Provenance, RNA)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "RNA" ~= "ribonucleic acid polymer with informational structural catalytic or regulatory functions"
  "messenger RNA" ~= "RNA carrying coding information for translation"
  "transfer RNA" ~= "adapter RNA coupling codon recognition to amino-acid delivery"
  "ribosomal RNA" ~= "structural and catalytic RNA component of ribosomes"
  "non-coding RNA" ~= "functional RNA not requiring translation into protein"
  "RNA processing" ~= "maturation modification or cleavage of precursor RNA"
  "RNA splicing" ~= "removal of introns and joining of exons as applicable"
  "RNA editing" ~= "post-transcriptional alteration of RNA sequence information"
  "RNA turnover" ~= "regulated degradation and replacement controlling RNA abundance"
  "RNA quality control" ~= "surveillance and management of aberrant RNA"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  nucleotide_structure_mapping: 0.99
  rna_type_mapping: 0.99
  transcription_processing_mapping: 0.99
  editing_modification_mapping: 0.99
  translation_role_mapping: 0.99
  regulatory_rna_mapping: 0.99
  interaction_localisation_mapping: 0.99
  turnover_quality_control_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_rna_observation:
    MAP rna_identity
    MAP sequence
    MAP structure
    MAP rna_type
    MAP localisation
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON rna_processing_event:
    UPDATE processing_state
    UPDATE splice_state
    UPDATE isoform_state
    UPDATE modification_state
    PRESERVE provenance
  ON regulatory_interaction:
    UPDATE binding_partner
    UPDATE target_state
    UPDATE expression_effect
    PRESERVE provenance
  ON rna_turnover_event:
    UPDATE stability
    UPDATE degradation_state
    UPDATE abundance
    UPDATE quality_control_state
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_RNA_ONTOLOGY
  reasoning_mode: RNA_SEQUENCE_STRUCTURE_FUNCTION_RELATIONAL
  preserve: [typed_entities, rna_identity, nucleotide_state, sequence, structure, rna_type, transcription_state, processing_state, splice_state, editing_state, modification_state, translation_role, regulatory_role, interaction_state, localisation, turnover_state, quality_control_state, evidence, uncertainty, confidence, provenance]
  infer: [sequence_structure_dependencies, processing_isoform_relationships, editing_effects, modification_effects, translation_role, regulatory_targeting, interaction_dependencies, localisation_effects, turnover_state, evidence_strength]
  prohibit: [invented_rna_sequences, fabricated_isoforms, unsupported_rna_targets, assumed_expression_without_evidence, unsupported_modification_state, unsupported_causal_claims, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + RNA_STRUCTURE_TYPES + TRANSCRIPTION_PROCESSING + EDITING_MODIFICATION + MRNA_TRNA_RRNA + NONCODING_REGULATION + INTERACTIONS_LOCALISATION + TURNOVER_QUALITY_CONTROL + EVIDENCE_UNCERTAINTY_PROVENANCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW