Spliceosome Ontology

FLOW ALGEBRA
TITLE: Spliceosome Ontology
VERSION: 1.0
DOMAIN: Biological Entities / Gene Expression Entities
SOURCE: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/gene-expression-entities/spliceosome-ontology.html
STATUS: Domain-grounded formalisation; source chapter not independently verified.
AUTHORS: Mark Higgins — Sky (Recursive AI)
LICENCE: Open research and educational reuse; refer to Kireth Research licence for applicable terms.

# 01 — PURPOSE
flow "SpliceosomeOntology" v1.0
purpose: Represent spliceosome components, assembly, catalysis, RNA splicing outcomes and evidence-aware inference.
context: Primarily nuclear spliceosomal pre-mRNA splicing in eukaryotes.

# 02 — TYPED ENTITIES
entity Spliceosome: RibonucleoproteinComplex
entity MajorSpliceosome: Spliceosome
entity MinorSpliceosome: Spliceosome
entity PreMRNA: RNA
entity MatureMRNA: RNA
entity Intron: RNARegion
entity Exon: RNARegion
entity FivePrimeSpliceSite: SequenceFeature
entity ThreePrimeSpliceSite: SequenceFeature
entity BranchPoint: SequenceFeature
entity PolypyrimidineTract: SequenceFeature
entity SmallNuclearRNA: RNA
entity SmallNuclearRNP: RibonucleoproteinComplex
entity U1snRNP: SmallNuclearRNP
entity U2snRNP: SmallNuclearRNP
entity U4snRNP: SmallNuclearRNP
entity U5snRNP: SmallNuclearRNP
entity U6snRNP: SmallNuclearRNP
entity U11snRNP: SmallNuclearRNP
entity U12snRNP: SmallNuclearRNP
entity U4atacsnRNP: SmallNuclearRNP
entity U6atacsnRNP: SmallNuclearRNP
entity SplicingFactor: Protein
entity SRProtein: SplicingFactor
entity HnRNP: RNA_BindingProtein
entity LariatIntermediate: RNAIntermediate
entity SpliceJunction: RNAFeature
entity SplicingEvent: BiologicalProcess
entity AlternativeSplicingEvent: SplicingEvent
entity SplicingIsoform: Transcript
entity EvidenceRecord: ProvenanceRecord

# 03 — CLASSIFICATION
subtype(MajorSpliceosome, Spliceosome)
subtype(MinorSpliceosome, Spliceosome)
major_components: [U1snRNP, U2snRNP, U4snRNP, U5snRNP, U6snRNP]
minor_components: [U11snRNP, U12snRNP, U4atacsnRNP, U5snRNP, U6atacsnRNP]
classification_rule: distinguish spliceosome type by splice-site recognition and component composition.
constraint: not all introns are removed by spliceosomes; self-splicing introns exist.

# 04 — STRUCTURAL RELATIONSHIPS
relation has_component(Spliceosome, SmallNuclearRNP)
relation binds(SmallNuclearRNP, RNARegion)
relation recognises(U1snRNP, FivePrimeSpliceSite)
relation recognises(U2snRNP, BranchPoint)
relation positions(U5snRNP, Exon)
relation participates_in(SplicingFactor, SplicingEvent)
relation produces(SplicingEvent, SpliceJunction)
relation derives_from(MatureMRNA, PreMRNA)
relation yields(AlternativeSplicingEvent, SplicingIsoform)
relation supported_by(Assertion, EvidenceRecord)

# 05 — INPUT SCHEMA
input:
  transcript_id: str
  organism: str
  genome_assembly: str?
  sequence: str?
  intron_coordinates: list[GenomicInterval]?
  exon_coordinates: list[GenomicInterval]?
  splice_site_annotations: list[SequenceFeature]?
  spliceosome_class: enum[major, minor, unknown]
  evidence: list[EvidenceRecord]
  biological_context: str?

# 06 — VALIDATION
validate coordinates_against_assembly
validate exon_intron_order_against_transcript_strand
validate nucleotide_alphabet: [A, C, G, U] for RNA sequence
validate splice_site_motifs_as_evidence_not_absolute_rules
validate transcript_and_isoform_identifiers
validate evidence_source_and_assay
on_failure: return structured_error; do_not_infer_unverified_splice_junction

# 07 — MAJOR SPLICEOSOME ASSEMBLY
state E: early recognition of 5-prime splice site and branch region
state A: stable U2 association with branch region
state B: U4/U6.U5 tri-snRNP recruited
state Bact: extensive rearrangement and activation
state C: first catalytic step completed
state P: exon ligation completed
state ILS: intron lariat spliceosome; disassembly follows
transition E -> A -> B -> Bact -> C -> P -> ILS
note: intermediate names and subdivisions vary between experimental schemes.

# 08 — CATALYTIC OPERATIONS
operation first_transesterification:
  input: pre_mRNA, branch_point_adenosine
  mechanism: branch-point 2-prime hydroxyl attacks 5-prime splice site
  output: lariat_intron_exon_intermediate, free_upstream_exon_3prime_OH
operation second_transesterification:
  input: lariat_intron_exon_intermediate, upstream_exon_3prime_OH
  mechanism: upstream exon 3-prime hydroxyl attacks 3-prime splice site
  output: ligated_exons, intron_lariat
constraint: reactions rearrange phosphodiester bonds; ATP-dependent remodelling supports assembly and fidelity.

# 09 — MINOR SPLICEOSOME
rule minor_splicing:
  when spliceosome_class == minor
  use U11/U12 recognition and U4atac/U6atac/U5 machinery
  preserve minor-intron-specific splice-site context
note: minor introns are not defined solely by a single dinucleotide pair.

# 10 — ALTERNATIVE SPLICING
patterns:
  - exon_skipping
  - alternative_5prime_splice_site
  - alternative_3prime_splice_site
  - intron_retention
  - mutually_exclusive_exons
rule isoform_generation:
  candidate_isoforms = enumerate_supported_junction_paths(pre_mRNA, evidence)
  reject paths_violating_strand_or_coordinate_constraints
  retain tissue_and_condition_specific_evidence
note: alternative splicing can alter coding sequence, UTRs, localisation or RNA stability.

# 11 — REGULATORY RELATIONSHIPS
relation enhances_splicing(SRProtein, SplicingEvent) [context_dependent]
relation modulates_splicing(HnRNP, SplicingEvent) [context_dependent]
relation influences(SpliceSiteStrength, SpliceSiteSelection)
relation influences(RNASecondaryStructure, SpliceSiteAccessibility)
relation influences(TranscriptionKinetics, CoTranscriptionalSplicing)
constraint: protein effects depend on binding position and biological context.

# 12 — INFERENCE RULES
rule canonical_major_candidate:
  if evidence_supports(U1snRNP, FivePrimeSpliceSite)
  and evidence_supports(U2snRNP, BranchPoint)
  then classify_candidate(major_spliceosome)
  confidence = combine_evidence_without_double_counting
rule confirmed_splice_junction:
  if split_read_support and valid_alignment and reproducible_context
  then assert splice_junction with provenance
rule splice_defect_candidate:
  if splice_site_variant and abnormal_junction_observed
  then infer potential_splicing_effect
  not infer clinical_pathogenicity_without_additional_evidence

# 13 — RECURSIVE REASONING
function resolve_splicing(transcript, evidence, depth):
  require depth <= MAX_DEPTH
  validate(transcript)
  identify_introns_and_candidate_sites(transcript)
  classify_splicing_machinery_if_supported(evidence)
  generate_candidate_junctions(transcript, evidence)
  evaluate_each_candidate_against_constraints
  recurse_on_isoform_subproblems_only_if_new_evidence_or_unresolved_regions
  memoise_by(transcript_id, evidence_version, biological_context)
  stop_on_fixed_point_or_depth_limit
  return ranked_supported_isoforms_with_provenance

# 14 — CONFIDENCE
CONFIDENCE:
  range: [0.0, 1.0]
  factors: [assay_quality, read_support, mapping_uniqueness, replication, biological_context, annotation_consistency]
  missing_evidence: unknown_not_false
  conflicting_evidence: preserve_conflict_and_reduce_certainty
  rule: never assign a numerical confidence without an explicit calibration method.

# 15 — SEMANTIC_EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  exact_aliases:
    - [spliceosomal_complex, spliceosome] # only in contexts where both denote the same complex
    - [pre_messenger_RNA, pre_mRNA]
  related_not_equivalent:
    - [spliceosome, ribosome]
    - [spliceosome, snRNP]
    - [splicing, transcription]
    - [intron_retention, exon_skipping]
  identity_requires: [organism, complex_type, molecular_context]

# 16 — FLOW_HASH
FLOW_HASH:
  algorithm: SHA-256
  canonicalise: [flow_version, entity_types, relations, rules, parameters, source_identifiers]
  exclude: [display_whitespace, execution_timestamp]
  output: compute_at_runtime
  purpose: reproducibility_and_change_detection

# 17 — UPDATE_MODEL
UPDATE_MODEL:
  trigger: [new_experimental_evidence, annotation_revision, new_isoform, changed_assembly, ontology_revision]
  steps:
    - validate_new_evidence
    - compare_provenance_and_version
    - update_affected_entities_and_relations
    - recompute_dependent_inferences
    - preserve_superseded_assertions_for_audit
    - regenerate_FLOW_HASH
  conflict_policy: retain_competing_supported_hypotheses

# 18 — AI_CONSUMPTION
AI_CONSUMPTION:
  outputs:
    - typed_entity_graph
    - spliceosome_classification
    - assembly_state_trace
    - splice_junction_candidates
    - transcript_isoform_relationships
    - evidence_and_confidence_records
    - provenance_and_version_metadata
  interoperability: [JSON-LD, RDF, OWL, graph_database]
  guardrails:
    - distinguish_observation_from_inference
    - do_not_invent_sequences_or_assay_results
    - distinguish_organism_specific_mechanisms
    - do_not_infer_disease_causation_from_splicing_change_alone

# 19 — EXAMPLE (SCHEMATIC)
example:
  input: pre_mRNA_with_two_exons_and_one_intron
  observed: supported_5prime_site, supported_branch_point, supported_3prime_site
  process: spliceosome_assembly -> activation -> lariat_formation -> exon_ligation
  output: ligated_exons + excised_intron_lariat
  status: illustrative_not_empirical_data

# 20 — OUTPUT CONTRACT
output:
  entity_graph: Graph
  splice_events: list[SplicingEvent]
  transcript_isoforms: list[SplicingIsoform]
  evidence: list[EvidenceRecord]
  confidence: optional[float]
  uncertainty_notes: list[str]
  flow_hash: str
  version: str

END FLOW ALGEBRA