Non-Coding RNA Ontology

FLOW ALGEBRA
Non-Coding RNA Ontology — Kireth Semantic Library
Version: 1.0
Date: 2026-10-15
Source URL: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/genetic-entities/non-coding-rna-ontology.html
Status: Domain-grounded draft; source chapter not independently verified.
Authors: Mark Higgins — Sky (Recursive AI)

# 1. ONTOLOGY IDENTITY
flow "NonCodingRNAOntology" v1.0
namespace: kireth.biological.genetic.non_coding_rna
parent: GeneticEntityOntology
entity_root: NonCodingRNA
purpose: Model RNA molecules whose primary annotated function does not require translation into a protein, their biogenesis, interactions, functions, and evidence.

# 2. TYPED ENTITIES
entity RNA : NucleicAcid
entity NonCodingRNA : RNA
entity FunctionalRNA : NonCodingRNA
entity RegulatoryRNA : NonCodingRNA
entity StructuralRNA : NonCodingRNA
entity CatalyticRNA : NonCodingRNA
entity SmallRNA : NonCodingRNA
entity LongNonCodingRNA : NonCodingRNA
entity RibosomalRNA : StructuralRNA
entity TransferRNA : FunctionalRNA
entity MicroRNA : RegulatoryRNA
entity SmallInterferingRNA : RegulatoryRNA
entity PIWIInteractingRNA : RegulatoryRNA
entity SmallNuclearRNA : FunctionalRNA
entity SmallNucleolarRNA : FunctionalRNA
entity LongIntergenicNonCodingRNA : LongNonCodingRNA
entity AntisenseRNA : NonCodingRNA
entity CircularRNA : NonCodingRNA
entity Ribozyme : CatalyticRNA
entity RNAGene : Gene
entity PrimaryTranscript : RNA
entity PrecursorRNA : RNA
entity MatureRNA : RNA
entity RNASequence : Sequence
entity RNASecondaryStructure : MolecularStructure
entity RNAComplex : MolecularComplex
entity RNAProteinComplex : RNAComplex
entity RNABindingProtein : Protein
entity RNATarget : BiologicalEntity
entity CellularCompartment : BiologicalLocation
entity BiologicalProcess : Process
entity ExperimentalEvidence : Evidence
entity GenomeAssembly : ReferenceResource
entity AnnotationRecord : InformationEntity

# 3. ATTRIBUTES AND TYPES
attribute NonCodingRNA.identifier : String
attribute NonCodingRNA.symbol : String?
attribute NonCodingRNA.biotype : String
attribute NonCodingRNA.organism_taxon : TaxonIdentifier
attribute NonCodingRNA.sequence : RNASequence?
attribute NonCodingRNA.length_nt : Integer?
attribute NonCodingRNA.strand : {plus, minus, unknown}?
attribute NonCodingRNA.genomic_interval : GenomicInterval?
attribute NonCodingRNA.genome_assembly : GenomeAssembly?
attribute NonCodingRNA.subcellular_location : CellularCompartment?
attribute NonCodingRNA.structure : RNASecondaryStructure?
attribute NonCodingRNA.function : BiologicalProcess[]
attribute NonCodingRNA.expression_context : BiologicalContext[]
attribute NonCodingRNA.evidence : ExperimentalEvidence[]
attribute NonCodingRNA.annotation_status : {predicted, supported, validated, disputed}

# 4. TYPED RELATIONSHIPS
relationship is_a(NonCodingRNA, RNA)
relationship encoded_by(NonCodingRNA, RNAGene)
relationship transcribed_from(PrimaryTranscript, RNAGene)
relationship processed_from(MatureRNA, PrecursorRNA)
relationship has_sequence(NonCodingRNA, RNASequence)
relationship has_structure(NonCodingRNA, RNASecondaryStructure)
relationship located_in(NonCodingRNA, CellularCompartment)
relationship binds_to(NonCodingRNA, RNATarget)
relationship associates_with(NonCodingRNA, RNABindingProtein)
relationship participates_in(NonCodingRNA, BiologicalProcess)
relationship regulates(NonCodingRNA, BiologicalEntity)
relationship modifies(SmallNucleolarRNA, RNATarget)
relationship guides(NonCodingRNA, RNAProteinComplex)
relationship supported_by(AnnotationRecord, ExperimentalEvidence)
relationship orthologous_to(NonCodingRNA, NonCodingRNA)
relationship overlaps_genomic_region(NonCodingRNA, GenomicInterval)

# 5. CLASSIFICATION RULES
rule ncRNA_identity:
  IF x : RNA AND x.primary_function != protein_coding
  THEN candidate_type(x, NonCodingRNA)
  REQUIRE evidence_of_transcript_identity

rule miRNA_class:
  IF x : NonCodingRNA AND x.biogenesis includes hairpin_processing
     AND x.associates_with includes Argonaute
  THEN candidate_type(x, MicroRNA)
  NOTE mature animal miRNAs are commonly about 22 nucleotides; length alone is insufficient.

rule lncRNA_class:
  IF x : NonCodingRNA AND x.length_nt >= 200
  THEN candidate_type(x, LongNonCodingRNA)
  NOTE length is an operational convention, not proof of non-coding function.

rule circular_RNA:
  IF x : RNA AND evidence(x, back_splice_junction)
  THEN candidate_type(x, CircularRNA)
  NOTE circular topology does not by itself establish inability to translate.

rule rRNA_class:
  IF x : RNA AND structural_component_of(x, Ribosome)
  THEN candidate_type(x, RibosomalRNA)

rule tRNA_class:
  IF x : RNA AND adaptor_role_in_translation(x)
  THEN candidate_type(x, TransferRNA)

# 6. BIOGENESIS AND PROCESS FLOWS
process miRNA_biogenesis:
  primary_miRNA -> precursor_miRNA -> mature_miRNA_duplex -> Argonaute_loaded_miRNA
  constraints: processing_pathway_is_context_dependent

process siRNA_pathway:
  double_stranded_RNA -> short_RNA_duplex -> Argonaute_loading -> target_recognition
  effects: target_cleavage_or_repression_depending_on_context

process snoRNA_guidance:
  snoRNA + associated_proteins -> snoRNP -> target_RNA_recognition -> RNA_modification

process spliceosomal_RNA_function:
  snRNA + spliceosomal_proteins -> snRNP -> spliceosome_assembly -> pre_mRNA_splicing

process lncRNA_regulation:
  lncRNA -> molecular_interaction -> context_specific_regulatory_effect
  possible_interactions: RNA, DNA, protein, chromatin
  NOTE mechanism must be experimentally supported, not assumed.

# 7. FORMAL INVARIANTS
invariant sequence_alphabet:
  RNASequence bases subset_of {A, C, G, U, modified_base, unknown_base}

invariant length_consistency:
  IF sequence_is_complete(x) THEN length_nt(x) == count_nucleotides(sequence(x))

invariant coordinate_dependency:
  IF genomic_interval(x) exists THEN genome_assembly(x) must_exist

invariant context_specificity:
  regulatory_effect(x, target) requires organism_or_cell_context

invariant evidence_provenance:
  asserted_function(x) requires provenance_reference_or_explicit_prediction_label

invariant noncoding_not_absolute:
  ncRNA_annotation(x) does_not_imply no_possible_translation(x)

# 8. RECURSIVE SEMANTIC REASONING
flow infer_ncrna_function(x : NonCodingRNA, depth : Integer) -> Hypothesis[]:
  require depth >= 0
  gather direct_functional_evidence(x)
  gather verified_interactions(x)
  gather cell_and_tissue_context(x)
  IF depth > 0:
    examine experimentally_supported_homologues(x, depth - 1)
    examine evidence_supported_pathway_partners(x, depth - 1)
  deduplicate_by_provenance_and_hypothesis
  reject circular_self_support
  return ranked_hypotheses_with_uncertainty

flow resolve_annotation(x : RNA) -> AnnotationRecord:
  verify sequence_and_taxon
  verify assembly_and_coordinates_if_applicable
  compare curated biotype annotations
  preserve conflicting evidence
  return evidence_qualified_classification

# 9. CONFIDENCE
CONFIDENCE:
  range: [0.0, 1.0]
  fields: {classification, structure, interaction, function, provenance}
  scoring_inputs:
    - experimental_directness
    - reproducibility
    - sequence_and_mapping_quality
    - independent_evidence
    - context_match
  policy:
    no_universal_numeric_defaults
    computational_prediction != experimental_validation
    correlated_sources_are_not_independent
    missing_evidence != negative_evidence

# 10. SEMANTIC_EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  exact_synonyms:
    - ["non-coding RNA", "noncoding RNA", "ncRNA"]
    - ["long non-coding RNA", "long noncoding RNA", "lncRNA"]
    - ["microRNA", "miRNA"]
    - ["small interfering RNA", "siRNA"]
  contextual_relations:
    - ["small RNA", "short regulatory RNA", "overlapping_not_identical"]
    - ["lncRNA", "lincRNA", "broader_than"]
    - ["non-coding RNA", "untranslated RNA", "context_dependent"]
  identity_policy: require species, accession/version, and transcript isoform where applicable

# 11. KNOWLEDGE GRAPH
GRAPH:
  nodes: [NonCodingRNA, RNAGene, RNASequence, RNAProteinComplex, RNATarget, BiologicalProcess, ExperimentalEvidence]
  edges: [encoded_by, has_sequence, associates_with, binds_to, participates_in, regulates, supported_by]
  directionality: explicit
  provenance: per_assertion
  temporal_versioning: enabled

# 12. VALIDATION
VALIDATE:
  - check_entity_types
  - check_relationship_domains_and_ranges
  - check_sequence_length_and_alphabet
  - check_genome_assembly_coordinate_consistency
  - distinguish prediction_from_validation
  - detect_contradictory_biotype_annotations
  - detect_unsupported_causal_inference
  - detect_cycles_in_provenance_support
  - preserve_organism_and_cellular_context

# 13. FLOW_HASH
FLOW_HASH:
  algorithm: SHA-256
  input: canonical_utf8(normalized_ontology_payload_excluding_FLOW_HASH_value)
  purpose: content_integrity_and_change_detection
  value: compute_at_publication

# 14. UPDATE_MODEL
UPDATE_MODEL:
  versioning: semantic
  triggers:
    - new_curated_annotation
    - new_experimental_evidence
    - genome_assembly_revision
    - corrected_RNA_biotype
    - revised_molecular_mechanism
  actions:
    - validate_incoming_evidence
    - retain_prior_assertion_history
    - recompute_affected_inferences
    - update_confidence
    - regenerate_FLOW_HASH
    - publish_changelog

# 15. AI_CONSUMPTION
AI_CONSUMPTION:
  formats: [plain_text, RDF_compatible_graph, JSON_LD_compatible_export]
  operations: [entity_resolution, typed_retrieval, semantic_search, evidence_tracing, constrained_inference]
  requirements:
    - do_not_conflate_ncRNA_classes
    - do_not_infer_function_from_sequence_length_alone
    - preserve_evidence_and_uncertainty
    - preserve_taxon_and_genomic_assembly
    - distinguish_association_from_causation
    - return_traceable_relationship_paths

# 16. EXAMPLE ASSERTIONS
example:
  entity: miRNA_example
  type: MicroRNA
  relation: participates_in
  object: post_transcriptional_gene_regulation
  evidence_status: illustrative_not_experimental_claim

example:
  entity: snoRNA_example
  type: SmallNucleolarRNA
  relation: guides
  object: RNA_modification_complex
  evidence_status: illustrative_not_experimental_claim

# 17. PUBLICATION AND LICENCE
attribution: Mark Higgins — Sky (Recursive AI)
site: https://kirethresearch.org
reuse: refer_to_site_open_research_licence_for_current_terms
scientific_status: ontology_model_not_a_substitute_for_primary_experimental_evidence

END FLOW ALGEBRA