Messenger Ribonucleoprotein Ontology

FLOW ALGEBRA
TITLE: Messenger Ribonucleoprotein Ontology
VERSION: 1.0
DOMAIN: Biological Entities / Gene Expression Entities
SOURCE_URL: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/gene-expression-entities/messenger-ribonucleoprotein-ontology.html
STATUS: Domain-grounded formalisation; source chapter not independently verified
AUTHORS: Mark Higgins — Sky (Recursive AI)
SITE: https://kirethresearch.org

# 01 PURPOSE
flow "MessengerRibonucleoproteinOntology" v1.0
purpose: represent mRNA-protein assemblies, their composition, maturation, transport, translation and turnover with typed, context-aware relations.

# 02 TYPES
type Entity = {id:str, label:str, provenance:str?}
type MessengerRNP <: Entity = {rna:MessengerRNA, proteins:set[RNABindingProtein], compartment:Compartment, state:AssemblyState}
type MessengerRNA <: Entity = {sequence:str?, transcript_id:str?, splicing_status:SplicingStatus, cap_status:bool?, polyA_status:bool?}
type RNABindingProtein <: Entity = {role:set[ProteinRole]}
type Compartment = Nucleus | NuclearPore | Cytoplasm | StressGranule | ProcessingBody | Other(str)
type AssemblyState = Nascent | Processing | ExportCompetent | Translating | Repressed | Stored | Decaying | Disassembled
type SplicingStatus = Unspliced | PartiallySpliced | Spliced | NotApplicable | Unknown
type ProteinRole = Splicing | Export | Localisation | Stability | Translation | Decay | Surveillance | Other(str)
type Interaction = {subject:Entity, predicate:Relation, object:Entity, context:Context, evidence:Evidence}
type Relation = CONTAINS_RNA | BINDS | ASSOCIATES_WITH | RECRUITS | RELEASES | EXPORTED_THROUGH | LOCALISED_TO | REGULATES | TRANSLATED_BY | TARGETED_FOR_DECAY | DERIVED_FROM
type Context = {organism:str?, cell_type:str?, compartment:Compartment?, condition:str?, time:str?}
type Evidence = {source:str, method:str?, confidence:float, observation:str?}

# 03 CORE AXIOMS
axiom A1: forall x:MessengerRNP, exists r:MessengerRNA where x.rna = r.
axiom A2: forall x:MessengerRNP, x.proteins is a set of RNA-associated proteins; protein occupancy may change over time.
axiom A3: MessengerRNP is an RNA-protein assembly, not synonymous with a ribosome or with naked mRNA.
axiom A4: The same mRNA may participate in distinct mRNP configurations at different stages.
axiom A5: Protein association alone does not prove direct RNA binding; distinguish direct binding from complex membership.

# 04 CLASSIFICATION
class NuclearMessengerRNP <: MessengerRNP where compartment = Nucleus
class ExportCompetentMessengerRNP <: MessengerRNP where state = ExportCompetent
class CytoplasmicMessengerRNP <: MessengerRNP where compartment = Cytoplasm
class TranslatingMessengerRNP <: MessengerRNP where state = Translating
class RepressedMessengerRNP <: MessengerRNP where state = Repressed
class DecayAssociatedMessengerRNP <: MessengerRNP where state = Decaying
class StressAssociatedMessengerRNP <: MessengerRNP where compartment = StressGranule

# 05 COMPOSITION AND RELATIONSHIPS
relation mRNP CONTAINS_RNA mRNA cardinality: exactly_one_primary_transcript_per_instance
relation mRNP ASSOCIATES_WITH RNABindingProtein cardinality: zero_or_more_observed; qualification: operational definition requires evidence of protein association
relation RNABindingProtein BINDS mRNA qualification: direct_binding_only_if_supported
relation mRNP LOCALISED_TO Compartment qualification: time_dependent
relation mRNP DERIVED_FROM precursor_mRNP qualification: assembly_history
relation mRNP TRANSLATED_BY Ribosome qualification: translating_state
relation mRNP TARGETED_FOR_DECAY RNA_DecayMachinery qualification: evidence_required

# 06 ASSEMBLY AND MATURATION
process AssembleNascentMRNP:
  input: nascent_mRNA, associated_proteins, nuclear_context
  precondition: transcription_in_progress OR transcript_available
  output: mRNP(state=Nascent, compartment=Nucleus)
  effects: associate_processing_and_packaging_factors

process ProcessTranscript:
  input: nuclear_mRNP
  possible_steps: capping, splicing, cleavage, polyadenylation, quality_control
  output: processed_mRNP
  constraints: processing_pathways_are_transcript_and_organism_dependent

process AcquireExportCompetence:
  input: processed_mRNP
  precondition: export_requirements_satisfied_in_context
  output: mRNP(state=ExportCompetent)
  caution: not_all_RNAs_require_identical_processing_or_export_factors

process NuclearExport:
  input: export_competent_mRNP
  mechanism: receptor_mediated_passage_via_nuclear_pore
  output: cytoplasmic_mRNP
  effects: remodel_associated_proteins

# 07 CYTOPLASMIC FATES
process TranslationInitiation:
  input: cytoplasmic_mRNP
  precondition: translation_permissive_context
  output: translating_mRNP
  effects: recruit_translation_factors_and_ribosome

process TranslationalRepression:
  input: cytoplasmic_mRNP
  triggers: regulatory_RNAs_or_proteins_or_cellular_conditions
  output: mRNP(state=Repressed)
  caution: repression_does_not_necessarily_imply_decay

process LocaliseTranscript:
  input: mRNP, localisation_signals, transport_factors
  output: spatially_localised_mRNP
  effect: compartment_or_subcellular_region_changed

process RNADegradation:
  input: decay_targeted_mRNP
  possible_routes: deadenylation, decapping, exonucleolytic_decay, endonucleolytic_cleavage, surveillance_pathways
  output: degraded_RNA_and_released_or_recycled_proteins
  caution: pathways_depend_on_transcript_and_context

# 08 STATE TRANSITIONS
transition Nascent -> Processing when transcript_processing_begins
transition Processing -> ExportCompetent when export_quality_requirements_met
transition ExportCompetent -> Cytoplasmic when nuclear_export_completed
transition Cytoplasmic -> Translating when initiation_complex_recruited
transition Translating -> Repressed when translation_suppressed
transition Repressed -> Translating when repression_reversed
transition Cytoplasmic -> Decaying when decay_pathway_committed
transition Repressed -> Decaying when decay_pathway_committed
transition Decaying -> Disassembled when RNA_destroyed_and_complex_dissociates
rule: transitions are possible, not mandatory or exhaustive; compartment and state are independent dimensions.

# 09 INFERENCE
rule R1: if mRNP has translation-associated ribosomes and active nascent peptide evidence then infer state=Translating with measured confidence.
rule R2: if transcript is enriched in a stress granule then infer stress-associated localisation, not automatic translational silencing for every molecule.
rule R3: if a protein co-immunoprecipitates with an mRNA then infer association, not necessarily direct binding.
rule R4: if a transcript is detected in the cytoplasm then infer export or cytoplasmic synthesis where biologically applicable; do not infer a unique export route.
rule R5: if transcript abundance decreases then do not infer accelerated decay without distinguishing altered synthesis from degradation.
rule R6: if splicing factors dissociate and export factors associate then infer maturation-associated remodelling when supported by temporal evidence.

# 10 VALIDATION
validate V1: mRNP.rna must resolve to an RNA transcript entity.
validate V2: confidence must lie in [0,1].
validate V3: every asserted direct RNA-protein binding requires direct-binding evidence or an explicit hypothesis tag.
validate V4: all genomic coordinates require reference assembly and coordinate convention.
validate V5: do not equate co-localisation with molecular interaction.
validate V6: distinguish molecule-level states from population-average measurements.
validate V7: track cell type, organism, condition and time when available.
validate V8: disallow simultaneous mutually exclusive states only within the same molecule, time and operational definition.

# 11 CONFIDENCE
CONFIDENCE:
  direct_structural_or_biochemical_evidence: high_when_replicated
  crosslinking_or_binding_assay: context_dependent
  co_purification: supports_association_not_necessarily_direct_binding
  imaging_colocalisation: supports_spatial_proximity
  computational_prediction: provisional_until_validated
  aggregation: evidence_weighted_with_dependency_checks
  missing_evidence: unknown_not_false

# 12 SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "messenger ribonucleoprotein" ~= "mRNP" when referring to mRNA-associated protein complex
  "messenger RNA" != "messenger ribonucleoprotein"
  "mRNP" != "ribosome"
  "RNA-binding protein" != "mRNP"
  "stress granule" != "mRNP"; granule may contain many mRNPs
  "processing body" != "RNA decay event"; localisation alone does not establish decay
  alias_resolution: organism_and_context_sensitive

# 13 RECURSIVE REASONING
recursive ResolveMRNP(entity, depth, visited):
  if depth <= 0 or entity.id in visited: return []
  visited.add(entity.id)
  neighbours = typed_relationships(entity)
  return neighbours + union(ResolveMRNP(n.object, depth-1, visited) for n in neighbours)
termination: bounded_depth_and_cycle_detection
invariant: preserve_evidence_context_and_relation_type_across_recursion

# 14 PROVENANCE
PROVENANCE:
  each_assertion: source_identifier, evidence_method, observation_date?, organism?, cell_type?, condition?
  transcript_identifiers: versioned_when_possible
  protein_identifiers: namespace_and_version_when_possible
  inferred_assertions: record_rule_and_parent_evidence
  uncertainty: retain_conflicting_results_instead_of_overwriting

# 15 FLOW HASH
FLOW_HASH:
  algorithm: SHA-256
  canonical_input: normalised_flow_text_excluding_computed_hash_value
  encoding: UTF-8
  normalisation: stable_line_endings_and_field_order
  purpose: detect_changes_and_support_version_integrity
  hash_value: computed_by_publishing_pipeline

# 16 UPDATE MODEL
UPDATE_MODEL:
  mode: versioned_append_with_supersession
  triggers: new_experimental_evidence, revised_transcript_annotation, corrected_relation, ontology_revision
  procedure:
    - validate_new_evidence
    - compare_existing_assertions
    - retain_provenance_and_previous_version
    - update_confidence_and_context
    - recalculate_FLOW_HASH
    - publish_change_log
  conflict_policy: preserve_disagreement_until_resolved

# 17 AI CONSUMPTION
AI_CONSUMPTION:
  entity_resolution: typed_identifiers_and_context
  retrieval: semantic_graph_traversal
  output: assertions_with_provenance_and_confidence
  reasoning: rule_based_and_evidence_weighted
  safeguards: do_not_promote_predictions_to_observed_facts
  interoperability: map_to_relevant_RNA_protein_and_gene_expression_ontologies_when_verified
  recursive_depth: bounded
  use_cases: gene_expression_research, RNA_transport, translational_regulation, RNA_decay, knowledge_graphs

# 18 EXAMPLE
example "cytoplasmic translation":
  entities:
    - transcript: mRNA_X
    - assembly: mRNP_X
    - machinery: ribosome_Y
  facts:
    - mRNP_X CONTAINS_RNA mRNA_X
    - mRNP_X ASSOCIATES_WITH translation_initiation_factor
    - mRNP_X TRANSLATED_BY ribosome_Y when active_translation_evidence_present
  inference: state(mRNP_X)=Translating only_with_sufficient_evidence
  confidence: evidence_dependent

# 19 LIMITATIONS
limitations:
  - conceptual ontology, not a validated executable program or laboratory protocol
  - not every mRNA follows the same maturation, export, storage or degradation route
  - association, binding, localisation and causal regulation require distinct evidence
  - cell-specific pathways and exceptions must be modelled explicitly

END FLOW ALGEBRA