Nucleic Acid Ontology

FLOW ALGEBRA
Nucleic Acid Ontology — Macromolecular Entities
Kireth Semantic Library | Version 1.0 | 15 October 2026
Authors: Mark Anthony Higgins — Sky (Recursive AI)
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/macromolecular-entities/nucleic-acid-ontology-2.html

PURPOSE
Formalise nucleic acids, nucleotide composition, sequence, structure, molecular roles,
biochemical transformations, and evidence-aware semantic reasoning.
This is an original ontology model aligned to the linked chapter topic; it is not a
verbatim transcription of the chapter's embedded code.

FLOW "NucleicAcidOntology" v1.0

NAMESPACE
  biological_entity: BiologicalEntity
  macromolecule: Macromolecule
  nucleic_acid: NucleicAcid
  nucleotide: Nucleotide
  nucleoside: Nucleoside
  nucleobase: Nucleobase
  phosphate: PhosphateGroup
  pentose: PentoseSugar
  sequence: NucleotideSequence
  structure: MolecularStructure
  process: BiologicalProcess
  evidence: EvidenceRecord

TYPE SYSTEM
  entity NucleicAcid <: Macromolecule
    id: URI
    kind: enum {DNA, RNA, HYBRID, SYNTHETIC_ANALOGUE}
    strandedness: enum {SINGLE, DOUBLE, MIXED, UNKNOWN}
    topology: enum {LINEAR, CIRCULAR, BRANCHED, UNKNOWN}
    sequence: NucleotideSequence?
    length_nt: integer?
    organism: URI?
    cellular_location: URI?
    provenance: EvidenceRecord[]

  entity Nucleotide
    base: Nucleobase
    sugar: PentoseSugar
    phosphate_count: integer >= 1
    modifications: URI[]

  entity Nucleoside
    base: Nucleobase
    sugar: PentoseSugar

  entity Nucleobase
    identity: enum {ADENINE, GUANINE, CYTOSINE, THYMINE, URACIL, MODIFIED, OTHER}
    family: enum {PURINE, PYRIMIDINE, OTHER}

  entity PentoseSugar
    identity: enum {RIBOSE, DEOXYRIBOSE, MODIFIED}

  entity NucleotideSequence
    alphabet: enum {DNA, RNA, EXTENDED}
    symbols: string
    orientation: enum {FIVE_TO_THREE, THREE_TO_FIVE, UNKNOWN}
    reference: URI?

  entity EvidenceRecord
    source: URI
    method: string?
    timestamp: datetime?
    confidence: real in [0,1]
    limitations: string[]

RELATIONSHIP SIGNATURES
  HAS_MONOMER: NucleicAcid -> Nucleotide
  HAS_SEQUENCE: NucleicAcid -> NucleotideSequence
  HAS_BASE: Nucleotide -> Nucleobase
  HAS_SUGAR: Nucleotide -> PentoseSugar
  HAS_PHOSPHATE: Nucleotide -> PhosphateGroup
  LINKED_BY: Nucleotide x Nucleotide -> PhosphodiesterBond
  COMPLEMENTARY_TO: Nucleobase -> Nucleobase
  BASE_PAIRS_WITH: Nucleotide -> Nucleotide
  TRANSCRIBED_FROM: RNA -> DNA
  REPLICATED_FROM: DNA -> DNA
  TRANSLATED_INTO: MessengerRNA -> Polypeptide
  CATALYSES: Ribozyme -> BiologicalProcess
  ENCODES: NucleicAcid -> BiologicalProduct
  REGULATES: RegulatoryRNA -> BiologicalProcess
  LOCATED_IN: NucleicAcid -> CellularCompartment
  DERIVED_FROM: NucleicAcid -> NucleicAcid
  SUPPORTED_BY: Assertion -> EvidenceRecord

CLASSIFICATION RULES
  rule DNA_DEFAULT:
    IF acid.kind == DNA AND acid is canonical
    THEN expected_sugar = DEOXYRIBOSE
         expected_alphabet = {A,C,G,T}
    EXCEPT chemically_modified_or_noncanonical_instances

  rule RNA_DEFAULT:
    IF acid.kind == RNA AND acid is canonical
    THEN expected_sugar = RIBOSE
         expected_alphabet = {A,C,G,U}
    EXCEPT chemically_modified_or_noncanonical_instances

  rule PURINE:
    IF base.identity IN {ADENINE, GUANINE}
    THEN base.family = PURINE

  rule PYRIMIDINE:
    IF base.identity IN {CYTOSINE, THYMINE, URACIL}
    THEN base.family = PYRIMIDINE

  rule NUCLEOSIDE_VS_NUCLEOTIDE:
    IF component = base + sugar AND phosphate_count == 0
    THEN classify(component, Nucleoside)
    IF component = base + sugar + one_or_more_phosphates
    THEN classify(component, Nucleotide)

SEQUENCE AND STRUCTURE
  constraint VALID_DNA_SEQUENCE:
    canonical(DNA) -> all(symbol IN {A,C,G,T} for symbol IN sequence)
  constraint VALID_RNA_SEQUENCE:
    canonical(RNA) -> all(symbol IN {A,C,G,U} for symbol IN sequence)
  constraint SEQUENCE_LENGTH:
    length_nt = count_nucleotide_positions(sequence)
  constraint BACKBONE:
    canonical_polynucleotide -> successive_monomers_linked_by_3prime_5prime_phosphodiester_bonds
  rule CANONICAL_DNA_PAIRING:
    A <-> T
    G <-> C
  rule CANONICAL_RNA_PAIRING:
    A <-> U
    G <-> C
  note PAIRING_CONTEXT:
    Complementarity is context-dependent; wobble pairs, mismatches, and modified
    nucleotides can occur. Antiparallel orientation applies to canonical duplexes.
  note STRUCTURE_LEVELS:
    primary = covalent nucleotide sequence
    secondary = local base-pairing patterns
    tertiary = three-dimensional conformation
    quaternary = multi-chain or complex-level assembly where applicable

BIOLOGICAL SUBTYPES
  DNA:
    genomic_DNA; mitochondrial_DNA; chloroplast_DNA; plasmid_DNA; viral_DNA
  RNA:
    messenger_RNA; ribosomal_RNA; transfer_RNA; small_nuclear_RNA
    small_nucleolar_RNA; microRNA; small_interfering_RNA
    long_non_coding_RNA; ribozyme_RNA; viral_RNA
  caution:
    Subtypes overlap by role, location and origin; they are not necessarily disjoint.

BIOCHEMICAL TRANSFORMATIONS
  process DNA_REPLICATION:
    inputs: template_DNA, deoxyribonucleoside_triphosphates, replication_machinery
    outputs: daughter_DNA
    relation: REPLICATED_FROM(daughter_DNA, template_DNA)
    constraints: template_dependence, strand_polarity, fidelity_mechanisms

  process TRANSCRIPTION:
    inputs: DNA_template, ribonucleoside_triphosphates, RNA_polymerase
    outputs: RNA_transcript
    relation: TRANSCRIBED_FROM(RNA_transcript, DNA_template)

  process RNA_PROCESSING:
    possible_operations: capping, splicing, polyadenylation, editing, cleavage
    applicability: organism_and_RNA_type_dependent

  process REVERSE_TRANSCRIPTION:
    inputs: RNA_template, reverse_transcriptase, deoxyribonucleoside_triphosphates
    outputs: complementary_DNA
    note: occurs in specific biological and laboratory contexts

  process TRANSLATION:
    inputs: coding_mRNA, ribosome, charged_tRNAs, translation_factors
    outputs: polypeptide
    note: not every RNA is translated

  process NUCLEIC_ACID_DEGRADATION:
    agents: nucleases, chemical_hydrolysis, environmental_factors
    outputs: shorter_oligonucleotides_or_nucleotide_products

FUNCTIONAL SEMANTICS
  DNA -> information_storage_and_heritable_template [context_dependent]
  mRNA -> coding_information_carrier [where_coding]
  rRNA -> ribosome_structural_and_catalytic_component
  tRNA -> adaptor_in_translation
  regulatory_RNA -> expression_regulation [subtype_dependent]
  ribozyme -> RNA_based_catalysis
  viral_nucleic_acid -> viral_genome [DNA_or_RNA]

REASONING RULES
  rule COMPOSITION_INFERENCE:
    IF HAS_MONOMER(acid, nucleotide)
    THEN component_of(nucleotide, acid)

  rule DNA_RNA_DISTINCTION:
    IF canonical(acid) AND sugar = RIBOSE AND uracil_in_sequence
    THEN support_classification(acid, RNA)
    NOT assert_certain_without_context

  rule TRANSCRIPTION_PROVENANCE:
    IF TRANSCRIBED_FROM(rna, dna) AND SUPPORTED_BY(assertion, evidence)
    THEN propagate_provenance(rna, evidence)

  rule FUNCTIONAL_INFERENCE:
    IF subtype(rna, transfer_RNA) AND verified_identity(rna)
    THEN candidate_function(rna, translation_adaptor)

  rule NON_EQUIVALENCE:
    DNA != RNA
    nucleotide != nucleoside
    nucleic_acid != protein
    transcription != translation

SEMANTIC_EQUIVALENCE
  exact:
    "deoxyribonucleic acid" == "DNA"
    "ribonucleic acid" == "RNA"
    "messenger RNA" == "mRNA"
    "transfer RNA" == "tRNA"
    "ribosomal RNA" == "rRNA"
  contextual:
    "polynucleotide" ~ "nucleic acid" ONLY IF chemical_and_structural_scope_matches
    "genetic material" ~ "nucleic acid" ONLY IN specified_biological_context
  forbidden:
    "nucleotide" != "nucleic acid polymer"
    "nucleobase" != "nucleotide"

CONFIDENCE
  evidence_weight:
    experimentally_verified_sequence: HIGH
    curated_reference_annotation: HIGH
    computational_prediction: VARIABLE
    unverified_textual_assertion: LOW
  aggregation:
    confidence(assertion) = calibrated_evidence_aggregation(
      source_quality, method_reliability, independence, consistency, context
    )
  constraint:
    do_not_assign_numeric_certainty_without_calibration
    do_not_treat_correlated_sources_as_independent

RECURSIVE_REASONING
  input: nucleic_acid_entity
  repeat_until fixed_point OR iteration_limit:
    resolve_type_and_subtype()
    validate_composition_and_sequence()
    infer_structural_relations()
    infer_process_participation()
    check_evidence_and_conflicts()
    propagate_qualified_relationships()
  terminate_on: stable_graph OR unresolved_conflict OR iteration_limit
  safeguard: no_unbounded_self_inference

PROVENANCE_AND_VALIDATION
  require_source_for: sequence_claim, structural_claim, functional_claim
  detect: conflicting_sequence, invalid_alphabet, missing_orientation
  detect: unsupported_function, incorrect_monomer_classification
  preserve: source_URI, revision, method, evidence_timestamp
  report: inferred_vs_observed, uncertainty, exceptions

FLOW_HASH
  canonicalise:
    normalise_identifiers
    sort_unordered_assertions
    preserve_ordered_sequences
    include_ontology_version_and_rule_set
  digest: SHA256(canonical_serialisation)
  note: digest is computed by an implementation, not asserted as a fixed value here

UPDATE_MODEL
  on_new_evidence:
    verify_source()
    compare_with_existing_assertions()
    update_versioned_graph_without_destroying_provenance()
    recompute_affected_inferences()
    recalibrate_confidence()
    recompute_FLOW_HASH()
    log_changes_and_conflicts()

AI_CONSUMPTION
  expose:
    typed_entities
    typed_relationships
    validated_sequences
    qualified_inferences
    provenance_and_confidence
    contradictions_and_unknowns
    ontology_version
    FLOW_HASH
  restrictions:
    distinguish_observation_from_inference
    preserve_chemical_and_biological_context
    never_infer_specific_sequence_from_molecule_class_alone
    never_infer_gene_function_from_sequence_without_sufficient_evidence
    do_not_conflate_DNA_RNA_and_protein

OUTPUT
  entity_graph: validated_typed_graph
  reasoning_trace: evidence_linked_inference_steps
  confidence_report: calibrated_if_available
  update_log: versioned_changes
  flow_hash: computed_at_runtime

END FLOW