Genetic Entities

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

FLOW ALGEBRA
Genetic Entities — Kireth Semantic Library
Version: 1.0 | Date: 2026-10-15 | Encoding: UTF-8
Authors: Mark Anthony Higgins — Sky (Recursive AI)
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/genetic-entities.html
Scope: parent category of genetic entities; subordinate ontology definitions remain authoritative for specialised details.

flow "GeneticEntities" v1.0

# 01 — DOMAIN AND TYPES
type GeneticEntity <: BiologicalEntity
type SequenceEntity <: GeneticEntity
type StructuralEntity <: GeneticEntity
type FunctionalEntity <: GeneticEntity
type RegulatoryEntity <: GeneticEntity
type VariationEntity <: GeneticEntity
type MolecularEntity <: GeneticEntity

type Genome <: StructuralEntity
type Chromosome <: StructuralEntity
type Chromatid <: StructuralEntity
type Centromere <: StructuralEntity
type Telomere <: StructuralEntity
type Gene <: FunctionalEntity
type Allele <: VariationEntity
type Locus <: StructuralEntity
type DNA <: MolecularEntity
type RNA <: MolecularEntity
type MessengerRNA <: RNA
type TransferRNA <: RNA
type RibosomalRNA <: RNA
type MicroRNA <: RNA
type NonCodingRNA <: RNA
type Codon <: SequenceEntity
type Anticodon <: SequenceEntity
type Nucleotide <: MolecularEntity
type Nucleoside <: MolecularEntity
type BasePair <: StructuralEntity
type GeneticMarker <: VariationEntity
type RegulatorySequence <: RegulatoryEntity
type Promoter <: RegulatorySequence
type Enhancer <: RegulatorySequence
type SilencerSequence <: RegulatorySequence
type Exon <: SequenceEntity
type Intron <: SequenceEntity
type Operon <: FunctionalEntity

# 02 — ENTITY IDENTIFICATION
entity.id: string
entity.type: GeneticEntity
entity.label: string
entity.definition: string?
entity.organism: Taxon?
entity.reference_assembly: string?
entity.reference_sequence: string?
entity.coordinates: GenomicInterval?
entity.strand: {plus, minus, unknown}?
entity.version: string?
entity.provenance: EvidenceRecord[]
entity.confidence: real in [0,1]

# 03 — TYPED RELATIONSHIPS
relation contains(Genome, Chromosome)
relation contains(Chromosome, Gene)
relation located_at(Gene, Locus)
relation variant_of(Allele, Gene)
relation composed_of(DNA, Nucleotide)
relation composed_of(RNA, Nucleotide)
relation comprises(BasePair, Nucleotide)
relation encodes(Gene, RNA)
relation transcribed_from(RNA, DNA)
relation translated_from(Protein, MessengerRNA)
relation recognises(TransferRNA, Codon)
relation has_anticodon(TransferRNA, Anticodon)
relation regulates(RegulatorySequence, Gene)
relation initiates_transcription_at(Promoter, Gene)
relation modulates_expression_of(Enhancer, Gene)
relation represses_expression_of(SilencerSequence, Gene)
relation spliced_into(Exon, MatureRNA)
relation removed_during_splicing(Intron, PrecursorRNA)
relation marks(GeneticMarker, GenomicInterval)
relation organises(Operon, Gene)
relation caps(Telomere, Chromosome)
relation joins_sister_chromatids(Centromere, Chromatid)

# 04 — CONSTRAINTS
constraint C01: every entity.id is nonempty and unique within a dataset
constraint C02: every entity.type resolves to a declared or imported type
constraint C03: genomic coordinates require an assembly or reference sequence
constraint C04: genomic intervals satisfy start >= 0 and end > start
constraint C05: coordinates use declared zero-based half-open convention unless explicitly mapped
constraint C06: strand and reference identifiers must be preserved across transformations
constraint C07: an allele is defined relative to a locus or reference state
constraint C08: a codon is a triplet in a specified reading frame and sequence context
constraint C09: RNA does not universally imply protein-coding function
constraint C10: promoter, enhancer and silencer effects are context dependent
constraint C11: eukaryotic splicing and prokaryotic operons are not universal genetic features
constraint C12: evidence, predictions and confirmed observations remain distinguishable

# 05 — CLASSIFICATION
rule R01: is_a(x, MessengerRNA) -> is_a(x, RNA)
rule R02: is_a(x, TransferRNA) -> is_a(x, RNA)
rule R03: is_a(x, RibosomalRNA) -> is_a(x, RNA)
rule R04: is_a(x, MicroRNA) -> is_a(x, NonCodingRNA)
rule R05: is_a(x, Promoter) -> is_a(x, RegulatorySequence)
rule R06: is_a(x, Enhancer) -> is_a(x, RegulatorySequence)
rule R07: is_a(x, SilencerSequence) -> is_a(x, RegulatorySequence)
rule R08: variant_of(a,g) -> is_a(a, Allele) AND is_a(g, Gene)
rule R09: located_at(g,l) -> is_a(g, Gene) AND is_a(l, Locus)
rule R10: encodes(g,r) -> is_a(g, Gene) AND is_a(r, RNA)

# 06 — BIOLOGICAL PROCESSES
process replication:
  input: DNA_template, nucleotides, replication_machinery
  output: DNA_products
  condition: suitable biological context
  preserve: sequence provenance, strand orientation

process transcription:
  input: DNA_template, RNA_polymerase, ribonucleotides
  output: RNA_transcript
  condition: transcriptionally active region
  note: transcription products include coding and non-coding RNAs

process RNA_processing:
  input: precursor_RNA
  output: processed_RNA
  condition: organism and transcript specific
  note: splicing is not mandatory for all transcripts

process translation:
  input: coding_mRNA, ribosome, charged_tRNAs
  output: polypeptide
  condition: valid initiation and coding context
  note: genetic code exceptions and recoding must be modelled explicitly

process sequence_variation:
  input: reference_sequence, observed_sequence
  output: variant_call
  condition: reference alignment and quality evidence
  preserve: assembly, coordinates, sample provenance

# 07 — INFERENCE AND GRAPH TRAVERSAL
infer I01: contains(genome, chromosome) AND contains(chromosome, gene)
           -> member_of_genome(gene, genome)
infer I02: variant_of(allele, gene) AND located_at(gene, locus)
           -> associated_locus(allele, locus)
infer I03: regulates(sequence, gene) AND located_at(gene, locus)
           -> candidate_regulatory_target(sequence, locus)
           [requires context evidence; not proof of causal action]
infer I04: transcribed_from(rna, dna) AND reference_match(rna, dna)
           -> transcription_link_supported(rna, dna)

# 08 — SEMANTIC_EQUIVALENCE
semantic_equivalence:
  exact: identical referent, assembly, sequence version and biological context
  close: compatible descriptions requiring context validation
  related: associated but non-interchangeable concepts
  prohibited_merges:
    - Gene != Allele
    - Gene != Locus
    - DNA != RNA
    - Nucleotide != Nucleoside
    - Codon != Anticodon
    - Exon != Intron
    - Chromosome != Chromatid
    - GeneticMarker != causal_variant

# 09 — CONFIDENCE
CONFIDENCE:
  range: [0,1]
  evidence_levels: [experimental, curated, computational, inferred, unknown]
  combine: evidence-aware; never assume independent observations
  rule: inferred confidence cannot exceed the weakest essential unsupported premise
  rule: unknown evidence is not assigned certainty
  rule: confidence scores must declare calibration method if interpreted probabilistically

# 10 — RECURSIVE REASONING
recursive_traversal:
  seed: GeneticEntity
  edges: typed relationships
  visit_policy: track visited entity IDs and edge types
  max_depth: configurable positive integer
  termination: no new supported nodes OR depth limit reached
  cycles: allowed in graph; forbidden as unbounded recursion
  output: path, inference, evidence, uncertainty

# 11 — FLOW_HASH
FLOW_HASH:
  algorithm: SHA-256
  canonical_input: normalised ontology identifier + version + sorted typed assertions + rule definitions
  exclude: timestamps and non-semantic display formatting
  purpose: deterministic change detection and provenance
  warning: hash equality tests canonical content, not biological truth

# 12 — UPDATE_MODEL
UPDATE_MODEL:
  trigger: new sequence evidence OR annotation revision OR reference assembly change OR ontology revision
  steps:
    - validate source and licensing metadata
    - preserve prior version and provenance
    - reconcile stable identifiers
    - re-map assembly-dependent coordinates where needed
    - re-evaluate affected relationships and rules
    - recalculate confidence with documented evidence
    - regenerate FLOW_HASH
    - publish revision and change log
  invariant: never silently overwrite conflicting biological evidence

# 13 — AI_CONSUMPTION
AI_CONSUMPTION:
  interpretation: typed, evidence-qualified knowledge graph
  require: explicit entity IDs, relationship types and source provenance
  prohibit: treating candidate links as established facts
  output_fields:
    - entity_id
    - entity_type
    - label
    - relations
    - supporting_evidence
    - confidence
    - reference_context
    - ontology_version
    - flow_hash
  fail_safe: return unknown or unresolved when evidence is insufficient

# 14 — VALIDATION TESTS
test T01: MicroRNA subtype resolves to RNA and NonCodingRNA
test T02: Allele and Gene remain distinct entities
test T03: mismatched reference assemblies block direct coordinate equality
test T04: cyclic regulatory links terminate safely
test T05: changes to a semantic assertion alter FLOW_HASH
test T06: unverified regulatory prediction is not promoted to confirmed causality
test T07: source provenance survives updates and exports

# 15 — INTEROPERABILITY
mapping_targets:
  - Sequence Ontology (SO)
  - Gene Ontology (GO), for biological functions and processes
  - HGNC or relevant organism-specific nomenclature authorities
  - INSDC and reference assembly accessions
  - GA4GH variation representations where applicable
mapping_policy: external identifiers require explicit verified cross-references

END FLOW ALGEBRA