Eukaryotic Cell Ontology

AI SEARCH FLOW ALGEBRA
EUKARYOTIC CELL ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

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

FLOW "EukaryoticCellOntology" v4.0
DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / EUKARYOTIC_CELL
ONTOLOGY := EUKARYOTIC_CELL_ONTOLOGY

EUKARYOTIC_CELL := CELL_IDENTITY + PLASMA_MEMBRANE + CYTOPLASM + NUCLEUS + GENOME + CHROMATIN + MEMBRANE_BOUND_ORGANELLES + ENDOMEMBRANE_SYSTEM + CYTOSKELETON + TRANSPORT + METABOLISM + BIOENERGETICS + GENE_EXPRESSION + PROTEOSTASIS + SIGNALING + CELL_CYCLE + MITOSIS + MEIOSIS + DIFFERENTIATION + HOMEOSTASIS + CELL_DEATH + EVIDENCE + PROVENANCE

PURPOSE := IDENTIFY_EUKARYOTIC_CELL -> MAP_MEMBRANE_AND_COMPARTMENTS -> MAP_NUCLEUS_GENOME_AND_CHROMATIN -> MAP_ORGANELLES -> MAP_ENDOMEMBRANE_SYSTEM_AND_CYTOSKELETON -> MAP_TRANSPORT_METABOLISM_AND_ENERGY -> MAP_GENE_EXPRESSION_AND_PROTEOSTASIS -> MAP_SIGNALING -> MAP_CELL_CYCLE_AND_DIVISION -> MAP_DIFFERENTIATION -> MAP_HOMEOSTASIS_STRESS_AND_DEATH -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY EukaryoticCell
ENTITY PlasmaMembrane
ENTITY Cytoplasm
ENTITY Nucleus
ENTITY NuclearEnvelope
ENTITY NuclearPore
ENTITY Nucleolus
ENTITY Genome
ENTITY Chromosome
ENTITY Chromatin
ENTITY DNA
ENTITY RNA
ENTITY Gene
ENTITY Mitochondrion
ENTITY Chloroplast
ENTITY EndoplasmicReticulum
ENTITY GolgiApparatus
ENTITY Lysosome
ENTITY Peroxisome
ENTITY Endosome
ENTITY Vesicle
ENTITY Ribosome
ENTITY Cytoskeleton
ENTITY Microtubule
ENTITY ActinFilament
ENTITY IntermediateFilament
ENTITY Centrosome
ENTITY Transporter
ENTITY Receptor
ENTITY Signal
ENTITY Metabolism
ENTITY GeneExpression
ENTITY Protein
ENTITY CellCycle
ENTITY Mitosis
ENTITY Meiosis
ENTITY Cytokinesis
ENTITY Differentiation
ENTITY CellState
ENTITY CellAdhesion
ENTITY CellMigration
ENTITY Homeostasis
ENTITY CellStress
ENTITY Apoptosis
ENTITY CellDeath
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# IDENTITY / MEMBRANE / COMPARTMENTS
EukaryoticCell -> subtype_of -> Cell
EukaryoticCell -> contains -> MEMBRANE_BOUND_NUCLEUS
EUKARYOTIC_CELL_CONTEXT := ANIMAL_CELL | PLANT_CELL | FUNGAL_CELL | PROTIST_CELL | OTHER_EUKARYOTIC_CELL
EukaryoticCell -> exhibits -> COMPARTMENTALISED_CELLULAR_ORGANISATION
PlasmaMembrane -> separates -> CYTOPLASM + EXTRACELLULAR_ENVIRONMENT
MEMBRANE_FUNCTION := SELECTIVE_BARRIER | TRANSPORT | SIGNAL_RECEPTION | ADHESION | ELECTROCHEMICAL_GRADIENT_MAINTENANCE
Compartmentalisation -> enables -> PROCESS_SPECIALISATION + DISTINCT_LOCAL_CHEMICAL_ENVIRONMENTS + REGULATED_MOLECULAR_TRAFFICKING
IF PlasmaMembraneIntegrity decreases THEN CellularHomeostasis -> MAY_DECREASE

# NUCLEUS / GENOME
Nucleus -> contains -> NUCLEAR_GENOME + CHROMATIN + NUCLEOLUS
NuclearEnvelope -> separates -> NUCLEOPLASM + CYTOPLASM
NuclearPore -> mediates -> NUCLEOCYTOPLASMIC_TRANSPORT
Nucleolus -> participates_in -> RIBOSOMAL_RNA_PRODUCTION + RIBOSOME_SUBUNIT_ASSEMBLY
Genome -> contains -> CHROMOSOMES + GENES + REGULATORY_SEQUENCES
Chromosome -> composed_of -> DNA + ASSOCIATED_PROTEINS
Chromatin -> organises -> DNA -> within -> NUCLEUS
ChromatinState -> influences -> GENE_ACCESSIBILITY + GENE_EXPRESSION
GENETIC_INFORMATION_FLOW := DNA -> TRANSCRIPTION -> RNA -> RNA_PROCESSING -> NUCLEAR_EXPORT -> TRANSLATION -> PROTEIN
GeneRegulation -> controls -> TRANSCRIPTION + CHROMATIN_ACCESSIBILITY + RNA_PROCESSING + RNA_STABILITY + TRANSLATION

# ORGANELLES / CYTOSKELETON / TRANSPORT
Mitochondrion -> participates_in -> ATP_PRODUCTION + CENTRAL_METABOLISM + CELL_SIGNALING + CELL_DEATH_REGULATION
Mitochondrion -> contains -> MITOCHONDRIAL_GENOME_AS_APPLICABLE
Chloroplast -> present_in -> PHOTOSYNTHETIC_EUKARYOTIC_CELLS_AS_APPLICABLE
Chloroplast -> participates_in -> PHOTOSYNTHESIS + CARBON_FIXATION + BIOSYNTHESIS
ENDOMEMBRANE_SYSTEM := NUCLEAR_ENVELOPE + ENDOPLASMIC_RETICULUM + GOLGI_APPARATUS + ENDOSOMES + LYSOSOMES + VESICLES + PLASMA_MEMBRANE_RELATIONSHIPS
EndoplasmicReticulum -> participates_in -> PROTEIN_SYNTHESIS + PROTEIN_FOLDING + LIPID_SYNTHESIS
GolgiApparatus -> modifies_and_sorts -> PROTEINS_AND_LIPIDS
Lysosome -> participates_in -> DEGRADATION + RECYCLING
Peroxisome -> participates_in -> OXIDATIVE_AND_LIPID_METABOLISM
Cytoskeleton -> provides -> CELL_SHAPE + MECHANICAL_SUPPORT + ORGANELLE_POSITIONING + INTRACELLULAR_TRANSPORT + MOTILITY + DIVISION_SUPPORT
CYTOSKELETAL_COMPONENT := MICROTUBULE | ACTIN_FILAMENT | INTERMEDIATE_FILAMENT
MEMBRANE_TRANSPORT := SIMPLE_DIFFUSION | FACILITATED_DIFFUSION | ACTIVE_TRANSPORT | ENDOCYTOSIS | EXOCYTOSIS
VESICULAR_TRAFFICKING := CARGO_SELECTION -> VESICLE_BUDDING -> TRANSPORT -> TETHERING -> DOCKING -> MEMBRANE_FUSION

# METABOLISM / SIGNALING / CELL CYCLE
Metabolism -> transforms -> MATTER + ENERGY
EUKARYOTIC_CELL_METABOLISM := CATABOLISM + ANABOLISM + BIOSYNTHESIS + ENERGY_TRANSFER
MetabolicPathway -> may_be_compartmentalised_in -> CYTOSOL | MITOCHONDRION | CHLOROPLAST_AS_APPLICABLE | OTHER_COMPARTMENT
Proteostasis := PROTEIN_SYNTHESIS + FOLDING + MODIFICATION + TRAFFICKING + QUALITY_CONTROL + DEGRADATION
CellSignaling -> transfers -> BIOLOGICAL_INFORMATION
SIGNALING_FLOW := SIGNAL -> RECEPTOR -> TRANSDUCTION -> EFFECTOR -> CELLULAR_RESPONSE
CELLULAR_RESPONSE := GENE_EXPRESSION_CHANGE | METABOLIC_CHANGE | SECRETION | MOTILITY | DIVISION | DIFFERENTIATION | SURVIVAL | CELL_DEATH

CellCycle -> coordinates -> CELL_GROWTH + DNA_REPLICATION + CHROMOSOME_SEGREGATION + CELL_DIVISION
CELL_CYCLE_PHASE := G1 | S | G2 | M | G0_AS_APPLICABLE
Checkpoint -> assesses -> DNA_INTEGRITY + REPLICATION_COMPLETION + CELL_STATE + SPINDLE_ATTACHMENT_AS_APPLICABLE
IF CheckpointCriteria not_met THEN CellCycleProgression -> DELAY_OR_ARREST
Mitosis -> segregates -> DUPLICATED_CHROMOSOMES -> into -> DAUGHTER_NUCLEI
Cytokinesis -> partitions -> CYTOPLASM + CELLULAR_COMPONENTS -> into -> DAUGHTER_CELLS
Meiosis -> produces -> REDUCED_CHROMOSOME_SET_CELLS_OR_NUCLEI_AS_APPLICABLE
Meiosis -> contributes_to -> GENETIC_VARIATION

# DIFFERENTIATION / HOMEOSTASIS / DEATH
Differentiation -> changes -> CellState -> toward -> SPECIALISED_CELL_IDENTITY
Differentiation -> involves -> GENE_REGULATION + EPIGENETIC_CHANGE + SIGNALING + STRUCTURAL_REORGANISATION
CellState := GENOME_STATE + CHROMATIN_STATE + GENE_EXPRESSION_STATE + PROTEIN_STATE + METABOLIC_STATE + SIGNALING_STATE + MORPHOLOGY + CELL_CYCLE_STATE
CellAdhesion -> connects -> CELL_CELL | CELL_EXTRACELLULAR_MATRIX
CellMigration -> changes -> CELL_POSITION
MIGRATION_FLOW := POLARISATION -> PROTRUSION -> ADHESION -> FORCE_GENERATION -> REAR_DETACHMENT -> TRANSLOCATION
Homeostasis -> maintains -> INTERNAL_VARIABLE -> within -> FUNCTIONAL_RANGE
HOMEOSTATIC_VARIABLE := PH | ION_CONCENTRATION | OSMOTIC_STATE | ENERGY_STATE | REDOX_STATE | PROTEIN_QUALITY | ORGANELLE_QUALITY
STRESS_TYPE := OXIDATIVE | DNA_DAMAGE | PROTEOTOXIC | THERMAL | OSMOTIC | NUTRIENT | HYPOXIC
StressResponse -> may -> REPAIR | ADAPT | ARREST_CELL_CYCLE | ALTER_METABOLISM | TRIGGER_CELL_DEATH
Autophagy -> supports -> RECYCLING + QUALITY_CONTROL + STRESS_ADAPTATION
CELL_DEATH_TYPE := APOPTOSIS | NECROTIC_CELL_DEATH | OTHER_REGULATED_CELL_DEATH
Apoptosis -> regulated_process_of -> CELL_DEATH

# EVIDENCE / UNCERTAINTY / PROVENANCE
EukaryoticCellClaim -> supported_by -> Evidence
EVIDENCE_TYPE := MICROSCOPIC | ULTRASTRUCTURAL | MOLECULAR | GENETIC | BIOCHEMICAL | IMAGING | FUNCTIONAL | PERTURBATION | COMPUTATIONAL
Evidence -> has -> SOURCE + METHOD + CELL_OR_SAMPLE + CONTEXT + QUALITY + UNCERTAINTY
EUKARYOTIC_CELL_UNCERTAINTY := MEASUREMENT_UNCERTAINTY + CELL_TO_CELL_VARIABILITY + CELL_TYPE_UNCERTAINTY + CELL_STATE_UNCERTAINTY + IMAGING_OR_SEGMENTATION_UNCERTAINTY + MODEL_UNCERTAINTY
Provenance -> records -> CELL_IDENTITY + TAXONOMIC_CONTEXT + CELL_TYPE + CELL_STATE + ORGANELLE_STATE + METHOD + OBSERVATION + EXPERIMENT + TIME + ENVIRONMENT + VERSION
EukaryoticCell -> linked_to -> Provenance

# REASONING
EUKARYOTIC_CELL_REASONING := IDENTIFY_CELL -> CLASSIFY_EUKARYOTIC_CONTEXT -> MAP_PLASMA_MEMBRANE -> MAP_COMPARTMENTS -> MAP_NUCLEUS_GENOME_AND_CHROMATIN -> MAP_MITOCHONDRIA_AND_OTHER_ORGANELLES -> MAP_ENDOMEMBRANE_SYSTEM -> MAP_CYTOSKELETON -> MAP_TRANSPORT_AND_VESICULAR_TRAFFICKING -> MAP_METABOLISM_AND_BIOENERGETICS -> MAP_GENE_EXPRESSION_AND_PROTEOSTASIS -> MAP_SIGNALING -> MAP_CELL_CYCLE_MITOSIS_AND_MEIOSIS -> MAP_DIFFERENTIATION -> MAP_ADHESION_AND_MIGRATION -> MAP_HOMEOSTASIS_AND_STRESS -> MAP_CELL_DEATH -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF NuclearEnvelopeIntegrity changes THEN NucleocytoplasmicOrganisation -> MAY_CHANGE
IF ChromatinState changes THEN GeneExpression -> MAY_CHANGE
IF MitochondrialFunction decreases THEN CellularEnergyState -> MAY_DECREASE
IF EndomembraneTrafficking changes THEN ProteinLocalizationOrSecretion -> MAY_CHANGE
IF Cytoskeleton changes THEN CellShapeTransportMigrationOrDivision -> MAY_CHANGE
IF CellCycleCheckpoint fails THEN GenomeIntegrityRisk -> MAY_INCREASE
IF Stress exceeds_homeostatic_capacity THEN CellState -> MAY_TRANSITION
IF Evidence insufficient THEN EukaryoticCellClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS / EQUIVALENCE
RELATION subtype_of(EukaryoticCell, Cell)
RELATION contains(EukaryoticCell, Nucleus)
RELATION separates(PlasmaMembrane, Cytoplasm, ExtracellularEnvironment)
RELATION contains(Nucleus, Genome)
RELATION organises(Chromatin, DNA)
RELATION mediates(NuclearPore, NucleocytoplasmicTransport)
RELATION participates_in(Mitochondrion, EnergyMetabolism)
RELATION participates_in(Chloroplast, Photosynthesis)
RELATION modifies_and_sorts(GolgiApparatus, CellularCargo)
RELATION degrades(Lysosome, CellularMaterial)
RELATION organises(Cytoskeleton, CellShape)
RELATION transports(Vesicle, Cargo)
RELATION transforms(Metabolism, Matter, Energy)
RELATION detects(Receptor, Signal)
RELATION coordinates(CellCycle, CellDivision)
RELATION segregates(Mitosis, Chromosome)
RELATION contributes_to(Meiosis, GeneticVariation)
RELATION changes(Differentiation, CellState)
RELATION maintains(Homeostasis, InternalVariable)
RELATION terminates(CellDeath, CellularLivingState)
RELATION supports(Evidence, EukaryoticCellClaim)
RELATION records(Provenance, EukaryoticCell)

SEMANTIC_EQUIVALENCE:
  "eukaryotic cell" ~= "cell containing a membrane-bound nucleus"
  "nuclear envelope" ~= "double membrane boundary surrounding the nucleus"
  "nuclear pore" ~= "regulated transport channel of the nuclear envelope"
  "chromatin" ~= "DNA-protein complex organising nuclear genetic material"
  "endomembrane system" ~= "interacting membrane compartments involved in synthesis trafficking and degradation"
  "mitochondrion" ~= "membrane-bound organelle central to eukaryotic cellular energy metabolism"
  "vesicular trafficking" ~= "transport of cargo between membrane-bound compartments"
  "mitosis" ~= "eukaryotic nuclear chromosome segregation process"
  "meiosis" ~= "reductional and equational divisions associated with sexual reproduction"
  "eukaryotic compartmentalisation" ~= "spatial separation of cellular processes by membrane-bound compartments"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  identity_membrane_mapping: 0.99
  nucleus_genome_mapping: 0.99
  organelle_mapping: 0.99
  endomembrane_cytoskeleton_mapping: 0.99
  transport_metabolism_mapping: 0.99
  signaling_mapping: 0.99
  cell_cycle_division_mapping: 0.99
  differentiation_homeostasis_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_eukaryotic_cell:
    MAP taxonomic_context
    MAP cell_type
    MAP nuclear_state
    MAP organelle_state
    MAP cell_state
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON new_cell_observation:
    UPDATE membrane_state
    UPDATE chromatin_state
    UPDATE organelle_state
    UPDATE metabolic_state
    UPDATE signaling_state
    UPDATE uncertainty
    PRESERVE provenance
  ON cell_cycle_transition:
    UPDATE cell_cycle_phase
    UPDATE chromosome_state
    UPDATE spindle_state
    UPDATE division_state
    PRESERVE provenance
  ON new_experimental_evidence:
    UPDATE cellular_relationships
    UPDATE evidence_quality
    UPDATE confidence
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_EUKARYOTIC_CELL_ONTOLOGY
  reasoning_mode: COMPARTMENTALISED_CELLULAR_RELATIONAL
  preserve: [typed_entities, cell_identity, taxonomic_context, membrane_state, nuclear_state, genome_and_chromatin, organelle_relationships, endomembrane_relationships, cytoskeletal_state, metabolic_state, signaling_state, cell_cycle_state, differentiation_state, evidence, uncertainty, confidence, provenance]
  infer: [compartment_function_dependencies, chromatin_expression_dependencies, organelle_function_dependencies, trafficking_dependencies, metabolic_dependencies, signaling_effects, cell_cycle_state, differentiation_state, stress_response, evidence_strength]
  prohibit: [invented_cell_observations, assuming_all_eukaryotic_cells_have_identical_organelles, fabricated_organelle_relationships, unsupported_cell_state, unsupported_causality, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + IDENTITY_MEMBRANE_COMPARTMENTS + NUCLEUS_GENOME_CHROMATIN + ORGANELLES_ENDOMEMBRANE_CYTOSKELETON + TRANSPORT_METABOLISM_SIGNALING + CELL_CYCLE_DIVISION + DIFFERENTIATION_HOMEOSTASIS_DEATH + EVIDENCE_UNCERTAINTY_PROVENANCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW