Cell Nucleus Ontology

AI SEARCH FLOW ALGEBRA
CELL NUCLEUS ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

SOURCE
https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/cell-biology/cell-nucleus-ontology.html

FLOW "CellNucleusOntology" v4.0
DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / CELL_NUCLEUS
ONTOLOGY := CELL_NUCLEUS_ONTOLOGY

CELL_NUCLEUS := NUCLEAR_IDENTITY + NUCLEAR_ENVELOPE + NUCLEAR_PORES + NUCLEOPLASM + CHROMATIN + CHROMOSOMES + GENOME + NUCLEAR_ARCHITECTURE + DNA_REPLICATION + DNA_REPAIR + TRANSCRIPTION + RNA_PROCESSING + RNA_EXPORT + NUCLEOLUS + RIBOSOME_BIOGENESIS + EPIGENETIC_REGULATION + GENE_REGULATION + NUCLEAR_TRANSPORT + CELL_CYCLE_DYNAMICS + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE := IDENTIFY_NUCLEUS -> MAP_NUCLEAR_BOUNDARY_AND_PORES -> MAP_NUCLEOPLASM_AND_ARCHITECTURE -> MAP_GENOME_CHROMATIN_AND_CHROMOSOMES -> MAP_DNA_REPLICATION_AND_REPAIR -> MAP_TRANSCRIPTION_AND_RNA_PROCESSING -> MAP_NUCLEOCYTOPLASMIC_TRANSPORT -> MAP_NUCLEOLUS_AND_RIBOSOME_BIOGENESIS -> MAP_EPIGENETIC_AND_GENE_REGULATION -> MAP_CELL_CYCLE_NUCLEAR_DYNAMICS -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY CellNucleus
ENTITY NuclearEnvelope
ENTITY NuclearPoreComplex
ENTITY NuclearLamina
ENTITY Nucleoplasm
ENTITY Genome
ENTITY Chromosome
ENTITY Chromatin
ENTITY Euchromatin
ENTITY Heterochromatin
ENTITY DNA
ENTITY Gene
ENTITY RegulatorySequence
ENTITY ChromosomeTerritory
ENTITY NuclearBody
ENTITY Nucleolus
ENTITY RNA
ENTITY Transcription
ENTITY RNAProcessing
ENTITY Splicing
ENTITY RNAExport
ENTITY DNAReplication
ENTITY DNARepair
ENTITY EpigeneticState
ENTITY Histone
ENTITY HistoneModification
ENTITY DNA_Methylation
ENTITY TranscriptionFactor
ENTITY NuclearTransport
ENTITY Importin
ENTITY Exportin
ENTITY CellCycle
ENTITY Mitosis
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# NUCLEAR STRUCTURE / GENOME
CellNucleus -> organelle_of -> EukaryoticCell
CellNucleus -> contains -> NUCLEAR_GENOME + CHROMATIN + NUCLEOPLASM + NUCLEAR_BODIES
NUCLEAR_FUNCTION := GENOME_STORAGE | DNA_REPLICATION | DNA_REPAIR | TRANSCRIPTION | RNA_PROCESSING | GENE_REGULATION | RIBOSOME_BIOGENESIS | GENOME_ORGANISATION

NuclearEnvelope -> surrounds -> CellNucleus
NuclearEnvelope -> separates -> NUCLEOPLASM + CYTOPLASM
NuclearPoreComplex -> spans -> NuclearEnvelope
NuclearPoreComplex -> regulates -> NUCLEOCYTOPLASMIC_TRANSPORT
NuclearLamina -> contributes_to -> NUCLEAR_SHAPE + MECHANICAL_STABILITY + CHROMATIN_ORGANISATION
IF NuclearEnvelopeIntegrity decreases THEN NuclearCompartmentalisation -> MAY_DECREASE

Genome -> organised_into -> Chromosome
Chromosome -> composed_of -> DNA + ASSOCIATED_PROTEINS
Gene -> region_of -> DNA
RegulatorySequence -> influences -> GENE_EXPRESSION

Chromatin -> composed_of -> DNA + HISTONES + OTHER_ASSOCIATED_PROTEINS
CHROMATIN_STATE := EUCHROMATIN | HETEROCHROMATIN | INTERMEDIATE_OR_CONTEXT_DEPENDENT_STATE
ChromatinAccessibility -> influences -> TRANSCRIPTION_FACTOR_ACCESS + GENE_EXPRESSION + DNA_REPAIR_ACCESS
ChromatinRemodelling -> changes -> NUCLEOSOME_POSITION + CHROMATIN_ACCESSIBILITY

# ARCHITECTURE / REPLICATION / REPAIR
NuclearArchitecture -> organises -> CHROMOSOMES + CHROMATIN_DOMAINS + NUCLEAR_BODIES
ChromosomeTerritory -> spatial_region_occupied_by -> CHROMOSOME
SpatialGenomeOrganisation -> may_influence -> GENE_REGULATION + REPLICATION + DNA_REPAIR

DNAReplication -> copies -> NUCLEAR_GENOME -> during -> S_PHASE
REPLICATION_FLOW := ORIGIN_LICENSING -> ORIGIN_ACTIVATION -> DNA_UNWINDING -> DNA_SYNTHESIS -> PROOFREADING -> COMPLETION
ReplicationAccuracy -> contributes_to -> GENOME_STABILITY
IF ReplicationStress increases THEN GenomeInstabilityRisk -> MAY_INCREASE

DNADamage -> may_activate -> DNA_DAMAGE_RESPONSE
DNA_REPAIR_PATHWAY := BASE_EXCISION_REPAIR | NUCLEOTIDE_EXCISION_REPAIR | MISMATCH_REPAIR | HOMOLOGOUS_RECOMBINATION | NON_HOMOLOGOUS_END_JOINING | OTHER_REPAIR_PATHWAY
RepairPathwayChoice -> depends_on -> DAMAGE_TYPE + CELL_CYCLE_STAGE + CHROMATIN_CONTEXT + AVAILABLE_MACHINERY
IF DNARepair fails THEN MutationOrGenomeInstabilityRisk -> MAY_INCREASE

# TRANSCRIPTION / RNA PROCESSING / TRANSPORT
Transcription -> synthesises -> RNA -> from -> DNA_TEMPLATE
TRANSCRIPTION_FLOW := PROMOTER_OR_REGULATORY_RECOGNITION -> INITIATION -> ELONGATION -> TERMINATION -> RNA_PRODUCT
TranscriptionRate -> influenced_by -> CHROMATIN_ACCESSIBILITY + TRANSCRIPTION_FACTORS + REGULATORY_SEQUENCES + CELL_SIGNALING

TranscriptionFactor -> binds -> DNA_REGULATORY_SEQUENCE | OTHER_REGULATORY_COMPONENT
TranscriptionFactor -> may -> ACTIVATE | REPRESS | MODULATE -> GENE_EXPRESSION

RNAProcessing -> modifies -> PRIMARY_RNA_TRANSCRIPT
RNA_PROCESSING_TYPE := CAPPING | SPLICING | POLYADENYLATION | RNA_EDITING_AS_APPLICABLE | RNA_MODIFICATION | RNA_QUALITY_CONTROL
Splicing -> removes -> INTRONS_AS_APPLICABLE
AlternativeSplicing -> may_generate -> MULTIPLE_RNA_ISOFORMS

RNAExport -> transports -> MATURE_OR_PROCESSING_APPROVED_RNA -> from -> NUCLEUS -> to -> CYTOPLASM
NuclearImport -> transports -> NUCLEAR_CARGO -> from -> CYTOPLASM -> to -> NUCLEUS
Importin -> mediates -> NUCLEAR_IMPORT
Exportin -> mediates -> NUCLEAR_EXPORT

# NUCLEOLUS / EPIGENETICS / CELL CYCLE
Nucleolus -> nuclear_body_involved_in -> RIBOSOME_BIOGENESIS
Nucleolus -> supports -> RRNA_TRANSCRIPTION + RRNA_PROCESSING + RIBOSOMAL_SUBUNIT_ASSEMBLY
RibosomalSubunit -> exported_to -> CYTOPLASM

EpigeneticState -> influences -> GENE_ACTIVITY -> without_necessarily_changing -> DNA_SEQUENCE
EPIGENETIC_MECHANISM := DNA_METHYLATION | HISTONE_MODIFICATION | CHROMATIN_REMODELLING | REGULATORY_RNA | HIGHER_ORDER_CHROMATIN_ORGANISATION
HistoneModification -> changes -> CHROMATIN_INTERACTIONS + PROTEIN_RECRUITMENT
EpigeneticEffect -> must_be_interpreted_with -> CELL_TYPE + GENOMIC_LOCATION + DEVELOPMENTAL_CONTEXT

GENE_REGULATION := CIS_REGULATORY_SEQUENCE + TRANSCRIPTION_FACTOR + CHROMATIN_STATE + EPIGENETIC_STATE + RNA_PROCESSING + NUCLEAR_ARCHITECTURE
IF RegulatoryState changes THEN GeneExpression -> MAY_CHANGE

CellCycle -> changes -> NUCLEAR_STATE
INTERPHASE_NUCLEAR_STATE := G1 | S | G2
DuringSPhase: DNAReplication -> ACTIVE
DuringMitosis: CHROMATIN -> CONDENSES_AS_APPLICABLE
DuringMitosis: CHROMOSOMES -> SEGREGATE
Mitosis -> segregates -> DUPLICATED_CHROMOSOMES
NuclearReassembly -> restores -> DAUGHTER_NUCLEAR_COMPARTMENTS

# HOMEOSTASIS / EVIDENCE / UNCERTAINTY
NuclearHomeostasis -> maintains -> GENOME_INTEGRITY + NUCLEAR_TRANSPORT + CHROMATIN_ORGANISATION + RNA_PROCESSING + NUCLEAR_PROTEIN_QUALITY
HOMEOSTATIC_PROCESS := DNA_REPAIR | RNA_QUALITY_CONTROL | PROTEIN_QUALITY_CONTROL | NUCLEAR_TRANSPORT_REGULATION | CHROMATIN_MAINTENANCE
IF NuclearHomeostasis fails THEN GeneExpressionOrGenomeIntegrity -> MAY_CHANGE

NuclearStress -> may_result_from -> DNA_DAMAGE + REPLICATION_STRESS + TRANSCRIPTIONAL_STRESS + PROTEOTOXIC_STRESS + NUCLEAR_ENVELOPE_DAMAGE
StressResponse -> may cause -> CELL_CYCLE_ARREST + DNA_REPAIR + GENE_EXPRESSION_CHANGE + SENESCENCE_OR_CELL_DEATH_AS_APPLICABLE

NucleusClaim -> supported_by -> Evidence
EVIDENCE_TYPE := MICROSCOPIC | ULTRASTRUCTURAL | MOLECULAR | GENETIC | GENOMIC | TRANSCRIPTOMIC | EPIGENOMIC | BIOCHEMICAL | FUNCTIONAL | COMPUTATIONAL
Evidence -> has -> SOURCE + METHOD + CELL_OR_NUCLEAR_SAMPLE + GENOMIC_REGION_IF_RELEVANT + CELL_STATE + CONDITION + QUALITY + UNCERTAINTY
NUCLEAR_UNCERTAINTY := MEASUREMENT_UNCERTAINTY + SPATIAL_ORGANISATION_UNCERTAINTY + CHROMATIN_STATE_UNCERTAINTY + CELL_TO_CELL_VARIABILITY + MODEL_UNCERTAINTY
Uncertainty -> qualifies -> NucleusClaim + ChromatinState + GeneExpression + NuclearTransport + GenomeOrganisation

Provenance -> records -> CELL_IDENTITY + NUCLEAR_STATE + GENOMIC_REGION + CHROMATIN_STATE + METHOD + CONDITION + MEASUREMENT + TIME + VERSION
CellNucleus -> linked_to -> Provenance

# REASONING / INFERENCE
CELL_NUCLEUS_REASONING := IDENTIFY_NUCLEUS -> MAP_NUCLEAR_ENVELOPE_AND_PORES -> MAP_NUCLEAR_LAMINA -> MAP_NUCLEOPLASM -> MAP_GENOME_CHROMOSOMES_AND_CHROMATIN -> MAP_NUCLEAR_ARCHITECTURE -> MAP_DNA_REPLICATION -> MAP_DNA_DAMAGE_AND_REPAIR -> MAP_TRANSCRIPTION -> MAP_RNA_PROCESSING -> MAP_NUCLEAR_IMPORT_AND_EXPORT -> MAP_NUCLEOLUS_AND_RIBOSOME_BIOGENESIS -> MAP_EPIGENETIC_REGULATION -> MAP_CELL_CYCLE_NUCLEAR_DYNAMICS -> MAP_NUCLEAR_HOMEOSTASIS -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

IF NuclearPoreFunction changes THEN NucleocytoplasmicTransport -> MAY_CHANGE
IF ChromatinAccessibility increases THEN RegulatoryFactorAccess -> MAY_INCREASE
IF DNAReplicationError persists THEN GenomeInstabilityRisk -> MAY_INCREASE
IF DNARepair fails THEN MutationRisk -> MAY_INCREASE
IF TranscriptionFactorNuclearLocalisation changes THEN GeneExpression -> MAY_CHANGE
IF RNAProcessing changes THEN MatureRNAOutput -> MAY_CHANGE
IF NucleolarFunction changes THEN RibosomeBiogenesis -> MAY_CHANGE
IF EpigeneticState changes THEN GeneRegulatoryState -> MAY_CHANGE
IF Evidence insufficient THEN NucleusClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS / EQUIVALENCE
RELATION organelle_of(CellNucleus, EukaryoticCell)
RELATION surrounds(NuclearEnvelope, CellNucleus)
RELATION spans(NuclearPoreComplex, NuclearEnvelope)
RELATION regulates(NuclearPoreComplex, NucleocytoplasmicTransport)
RELATION organises(NuclearLamina, Chromatin)
RELATION contains(CellNucleus, Genome)
RELATION composed_of(Chromosome, DNA)
RELATION composed_of(Chromatin, DNA)
RELATION copies(DNAReplication, NuclearGenome)
RELATION repairs(DNARepair, DNA)
RELATION synthesises(Transcription, RNA)
RELATION modifies(RNAProcessing, RNA)
RELATION transports(RNAExport, RNA)
RELATION supports(Nucleolus, RibosomeBiogenesis)
RELATION influences(EpigeneticState, GeneActivity)
RELATION changes(CellCycle, NuclearState)
RELATION supports(Evidence, NucleusClaim)
RELATION records(Provenance, CellNucleus)

SEMANTIC_EQUIVALENCE:
  "cell nucleus" ~= "membrane-bound eukaryotic organelle containing the nuclear genome"
  "nuclear envelope" ~= "double membrane boundary surrounding the nucleus"
  "nuclear pore complex" ~= "regulated macromolecular transport gateway across the nuclear envelope"
  "chromatin" ~= "DNA and associated proteins organising nuclear genetic material"
  "euchromatin" ~= "relatively accessible chromatin state as defined"
  "heterochromatin" ~= "relatively compact chromatin state as defined"
  "nucleolus" ~= "nuclear body central to ribosome biogenesis"
  "nuclear transport" ~= "regulated movement between nucleus and cytoplasm"
  "epigenetic regulation" ~= "gene regulation involving heritable or persistent molecular states without required DNA sequence change"
  "nuclear architecture" ~= "spatial organisation of nuclear components and genome"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  envelope_pore_mapping: 0.99
  genome_chromatin_mapping: 0.99
  architecture_mapping: 0.99
  replication_repair_mapping: 0.99
  transcription_rna_mapping: 0.99
  nucleolus_mapping: 0.99
  epigenetic_regulation_mapping: 0.99
  cell_cycle_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_nuclear_observation:
    MAP nuclear_state
    MAP envelope_state
    MAP chromatin_state
    MAP genome_organisation
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON DNA_damage_event:
    UPDATE damage_state
    UPDATE repair_state
    UPDATE genome_integrity
    PRESERVE provenance
  ON gene_regulatory_change:
    UPDATE chromatin_accessibility
    UPDATE transcription_factor_state
    UPDATE transcriptional_output
    PRESERVE provenance
  ON cell_cycle_transition:
    UPDATE nuclear_architecture
    UPDATE chromosome_state
    UPDATE envelope_state
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_CELL_NUCLEUS_ONTOLOGY
  reasoning_mode: NUCLEAR_GENOME_REGULATORY_RELATIONAL
  preserve: [typed_entities, nuclear_identity, envelope_state, pore_state, nuclear_architecture, genome, chromosome_state, chromatin_state, replication_state, repair_state, transcription_state, rna_processing_state, nucleolar_state, epigenetic_state, evidence, uncertainty, confidence, provenance]
  infer: [transport_dependencies, chromatin_expression_dependencies, replication_integrity_dependencies, repair_dependencies, transcriptional_effects, rna_processing_effects, nucleolar_function, cell_cycle_nuclear_state, evidence_strength]
  prohibit: [invented_nuclear_observations, unsupported_chromatin_state, fabricated_gene_regulation, assumed_dna_repair_outcome, unsupported_nuclear_architecture, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + NUCLEAR_STRUCTURE_GENOME + ARCHITECTURE_REPLICATION_REPAIR + TRANSCRIPTION_RNA_TRANSPORT + NUCLEOLUS_EPIGENETICS_CELL_CYCLE + HOMEOSTASIS_EVIDENCE_UNCERTAINTY + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW