Cell Ontology

AI SEARCH FLOW ALGEBRA
CELL ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

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

FLOW "CellOntology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / CELL
ONTOLOGY := CELL_ONTOLOGY

CELL :=
  CELL_IDENTITY + CELL_TYPE + CELL_BOUNDARY
  + CELLULAR_COMPONENTS + ORGANELLES + CYTOSKELETON
  + GENOME + GENE_EXPRESSION + METABOLISM
  + TRANSPORT + SIGNALING + CELL_STATE
  + CELL_CYCLE + DIVISION + DIFFERENTIATION
  + ADHESION + MIGRATION + HOMEOSTASIS
  + STRESS_RESPONSE + CELL_DEATH
  + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE :=
  IDENTIFY_CELL -> CLASSIFY_CELL_TYPE
  -> DEFINE_CELL_BOUNDARY -> MAP_CELLULAR_COMPONENTS
  -> MAP_GENOME_AND_GENE_EXPRESSION
  -> MAP_METABOLISM_AND_ENERGY
  -> MAP_TRANSPORT_AND_SIGNALING
  -> DEFINE_CELL_STATE -> MAP_CELL_CYCLE_AND_DIVISION
  -> MAP_DIFFERENTIATION_AND_CELL_FATE
  -> MAP_CELL_INTERACTIONS
  -> MAP_HOMEOSTASIS_STRESS_AND_DEATH
  -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY Cell
ENTITY CellIdentity
ENTITY CellType
ENTITY ProkaryoticCell
ENTITY EukaryoticCell
ENTITY CellBoundary
ENTITY CellMembrane
ENTITY Cytoplasm
ENTITY Organelle
ENTITY Nucleus
ENTITY Mitochondrion
ENTITY Ribosome
ENTITY Cytoskeleton
ENTITY Genome
ENTITY Chromosome
ENTITY DNA
ENTITY RNA
ENTITY Gene
ENTITY Protein
ENTITY Metabolism
ENTITY Transport
ENTITY Signal
ENTITY Receptor
ENTITY CellSignaling
ENTITY CellState
ENTITY CellCycle
ENTITY CellDivision
ENTITY Mitosis
ENTITY Meiosis
ENTITY Cytokinesis
ENTITY Differentiation
ENTITY CellFate
ENTITY CellAdhesion
ENTITY CellMigration
ENTITY Homeostasis
ENTITY CellStress
ENTITY CellDeath
ENTITY Apoptosis
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# IDENTITY / BOUNDARY / COMPONENTS
Cell -> has -> CellIdentity
Cell -> fundamental_unit_of -> CELLULAR_LIFE

CELL_TYPE := PROKARYOTIC | EUKARYOTIC

CellIdentity :=
  CELL_TYPE + SPECIES_OR_SOURCE
  + DEVELOPMENTAL_CONTEXT
  + LOCATION_OR_TISSUE_IF_RELEVANT
  + CELL_STATE

CellMembrane ->
  separates -> CELL_INTERIOR + EXTRACELLULAR_ENVIRONMENT

CELL_MEMBRANE_FUNCTION :=
  SELECTIVE_BARRIER | MATERIAL_TRANSPORT
  | SIGNAL_RECEPTION | CELL_ADHESION
  | ELECTROCHEMICAL_GRADIENT_MAINTENANCE

Cell ->
  contains -> Cytoplasm + GENETIC_MATERIAL
  + Ribosome + ORGANELLES_WHERE_APPLICABLE
  + Cytoskeleton_WHERE_APPLICABLE

IF MembraneIntegrity decreases
THEN CellularHomeostasis -> MAY_DECREASE

# ORGANELLES / CYTOSKELETON / GENOME
Organelle -> part_of -> Cell
Nucleus -> contains -> CHROMOSOMAL_DNA_IN_EUKARYOTES
Mitochondrion -> participates_in -> ENERGY_METABOLISM + CELLULAR_SIGNALING
Ribosome -> performs -> TRANSLATION

Cytoskeleton ->
  provides -> CELL_SHAPE + MECHANICAL_SUPPORT
  + INTRACELLULAR_TRANSPORT + MOTILITY + DIVISION_SUPPORT

CYTOSKELETAL_COMPONENT :=
  MICROTUBULE | ACTIN_FILAMENT | INTERMEDIATE_FILAMENT

Cell -> contains -> Genome
Genome -> contains -> Gene
Chromosome -> organises -> DNA
DNA -> stores -> GENETIC_INFORMATION

GENETIC_INFORMATION_FLOW :=
  DNA -> TRANSCRIPTION -> RNA -> TRANSLATION -> PROTEIN

GeneExpression -> produces -> FUNCTIONAL_RNA | PROTEIN
GeneRegulation -> controls -> EXPRESSION_LEVEL + TIMING + LOCATION

IF GeneExpression changes
THEN CellState -> MAY_CHANGE

# METABOLISM / TRANSPORT / SIGNALING
Metabolism -> transforms -> MATTER + ENERGY

CELL_METABOLISM :=
  CATABOLISM + ANABOLISM + BIOSYNTHESIS + ENERGY_TRANSFER

MetabolicState ->
  defined_by -> METABOLITE_LEVELS + PATHWAY_ACTIVITY + ENERGY_STATE

ATP ->
  commonly_supports -> ENERGY_REQUIRING_CELLULAR_PROCESS

TRANSPORT_TYPE :=
  SIMPLE_DIFFUSION | FACILITATED_DIFFUSION
  | ACTIVE_TRANSPORT | ENDOCYTOSIS
  | EXOCYTOSIS | VESICULAR_TRANSPORT

PassiveTransport ->
  follows -> ELECTROCHEMICAL_OR_CONCENTRATION_GRADIENT

ActiveTransport -> requires -> ENERGY_COUPLING

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

# CELL STATE / CYCLE / DIVISION / DIFFERENTIATION
CellState :=
  GENOME_STATE + GENE_EXPRESSION_STATE
  + PROTEIN_STATE + METABOLIC_STATE
  + SIGNALING_STATE + MORPHOLOGY
  + CELL_CYCLE_STATE

CELL_STATE_TYPE :=
  PROLIFERATING | QUIESCENT | DIFFERENTIATING
  | DIFFERENTIATED | ACTIVATED | STRESSED
  | SENESCENT | DYING

CellCycle ->
  coordinates -> CELL_GROWTH + DNA_REPLICATION
  + CHROMOSOME_SEGREGATION + CELL_DIVISION

CELL_CYCLE_PHASE := G1 | S | G2 | M | G0_AS_APPLICABLE

Checkpoint ->
  evaluates -> DNA_INTEGRITY + REPLICATION_COMPLETION
  + CELL_STATE + SPINDLE_ATTACHMENT_AS_APPLICABLE

IF CheckpointCriteria not_met
THEN CellCycleProgression -> DELAY_OR_ARREST

Mitosis -> segregates -> DUPLICATED_CHROMOSOMES
Cytokinesis -> partitions -> CELLULAR_CONTENT
Meiosis -> contributes_to -> GENETIC_VARIATION

Differentiation ->
  changes -> CellState -> toward -> SPECIALISED_CELL_IDENTITY

CellFate -> represents -> DEVELOPMENTAL_OUTCOME

# INTERACTIONS / HOMEOSTASIS / STRESS / DEATH
CellAdhesion ->
  links -> CELL_CELL | CELL_EXTRACELLULAR_MATRIX

CellAdhesion ->
  influences -> CELL_SHAPE + SIGNALING
  + POLARITY + MIGRATION + TISSUE_ORGANISATION

CellMigration -> changes -> CELL_POSITION

MIGRATION_FLOW :=
  POLARISATION -> PROTRUSION -> ADHESION
  -> FORCE_GENERATION -> DETACHMENT -> TRANSLOCATION

Homeostasis ->
  maintains -> INTRACELLULAR_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

CELL_DEATH_TYPE :=
  APOPTOSIS | NECROTIC_CELL_DEATH | OTHER_REGULATED_CELL_DEATH

Apoptosis -> regulated_process_of -> CellDeath

# PROKARYOTIC / EUKARYOTIC / EVIDENCE
ProkaryoticCell -> lacks -> MEMBRANE_BOUND_NUCLEUS
ProkaryoticCell ->
  contains -> CELL_MEMBRANE + CYTOPLASM
  + RIBOSOMES + GENETIC_MATERIAL

BinaryFission ->
  common_division_process_of -> MANY_PROKARYOTIC_CELLS

EukaryoticCell ->
  contains -> NUCLEUS + MEMBRANE_BOUND_ORGANELLES_AS_APPLICABLE

EukaryoticCompartmentalisation ->
  spatially_organises -> CELLULAR_PROCESSES

CellClaim -> supported_by -> Evidence

EVIDENCE_TYPE :=
  MICROSCOPIC | MOLECULAR | GENETIC
  | BIOCHEMICAL | FUNCTIONAL
  | PERTURBATION | IMAGING | COMPUTATIONAL

Evidence ->
  has -> SOURCE + METHOD + CELL_OR_SAMPLE
  + CONTEXT + QUALITY + UNCERTAINTY

CELL_UNCERTAINTY :=
  MEASUREMENT_UNCERTAINTY
  + CELL_TO_CELL_VARIABILITY
  + CELL_TYPE_CLASSIFICATION_UNCERTAINTY
  + CELL_STATE_UNCERTAINTY
  + MODEL_UNCERTAINTY

Provenance ->
  records -> CELL_IDENTITY + CELL_TYPE
  + SPECIES_OR_SOURCE + CELL_STATE
  + METHOD + OBSERVATION + EXPERIMENT
  + TIME + ENVIRONMENT + VERSION

Cell -> linked_to -> Provenance

# REASONING / INFERENCE
CELL_ONTOLOGY_REASONING :=
  IDENTIFY_CELL -> CLASSIFY_CELL_TYPE
  -> MAP_CELL_BOUNDARY -> MAP_CELLULAR_COMPONENTS
  -> MAP_ORGANELLES -> MAP_CYTOSKELETON
  -> MAP_GENOME -> MAP_GENE_EXPRESSION
  -> MAP_PROTEIN_STATE -> MAP_METABOLISM_AND_ENERGY
  -> MAP_TRANSPORT -> MAP_SIGNALING
  -> DEFINE_CELL_STATE -> MAP_CELL_CYCLE_AND_DIVISION
  -> MAP_DIFFERENTIATION_AND_CELL_FATE
  -> MAP_ADHESION_AND_MIGRATION
  -> MAP_CELL_INTERACTIONS
  -> MAP_HOMEOSTASIS_AND_STRESS
  -> MAP_CELL_DEATH -> ASSESS_EVIDENCE
  -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

IF CellMembrane integrity_decreases
THEN Homeostasis -> MAY_DECREASE

IF OrganelleState changes
THEN CellFunction -> MAY_CHANGE

IF GenomeState changes
THEN GeneExpressionOrCellFunction -> MAY_CHANGE

IF GeneExpression changes
THEN CellState -> MAY_CHANGE

IF EnergyState decreases
THEN EnergyDependentProcesses -> MAY_DECREASE

IF SignalingState changes
THEN CellBehaviour -> MAY_CHANGE

IF CellCycleCheckpoint fails
THEN GenomeIntegrityRisk -> MAY_INCREASE

IF Differentiation progresses
THEN CellIdentityAndFunction -> MAY_CHANGE

IF Stress exceeds_tolerance
THEN CellState -> MAY_TRANSITION_TO_ARREST_SENESCENCE_OR_DEATH

IF Evidence insufficient
THEN CellClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION has(Cell, CellIdentity)
RELATION subtype_of(ProkaryoticCell, Cell)
RELATION subtype_of(EukaryoticCell, Cell)
RELATION separates(CellMembrane, CellInterior, ExtracellularEnvironment)
RELATION contains(Cell, Organelle)
RELATION part_of(Organelle, Cell)
RELATION contains(Cell, Genome)
RELATION contains(Genome, Gene)
RELATION stores(DNA, GeneticInformation)
RELATION produces(GeneExpression, Protein)
RELATION transforms(Metabolism, Matter, Energy)
RELATION detects(Receptor, Signal)
RELATION changes(CellSignaling, CellState)
RELATION coordinates(CellCycle, CellDivision)
RELATION segregates(Mitosis, Chromosome)
RELATION changes(Differentiation, CellState)
RELATION links(CellAdhesion, Cell)
RELATION changes(CellMigration, CellPosition)
RELATION maintains(Homeostasis, IntracellularVariable)
RELATION terminates(CellDeath, CellularLivingState)
RELATION supports(Evidence, CellClaim)
RELATION records(Provenance, Cell)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "cell" ~= "fundamental cellular unit of life"
  "cell ontology" ~= "formal ontology of cellular entities and states"
  "cell membrane" ~= "plasma membrane"
  "cell state" ~= "integrated molecular metabolic structural and functional state of a cell"
  "cell cycle" ~= "ordered sequence of cell growth genome replication and division"
  "cell division" ~= "process producing daughter cells"
  "cell differentiation" ~= "transition toward specialised cellular identity"
  "cell signaling" ~= "cellular signal transduction and response"
  "cellular homeostasis" ~= "maintenance of intracellular conditions within functional ranges"
  "cell death" ~= "termination of the cellular living state"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  cell_identity_mapping: 0.99
  boundary_component_mapping: 0.99
  organelle_genome_mapping: 0.99
  metabolism_transport_mapping: 0.99
  signaling_state_mapping: 0.99
  cycle_division_mapping: 0.99
  differentiation_interaction_mapping: 0.99
  homeostasis_death_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_cell:
    MAP cell_identity
    MAP cell_type
    MAP cellular_components
    MAP genome
    MAP cell_state
    UPDATE confidence
    RECOMPUTE FLOW_HASH

  ON new_cell_observation:
    UPDATE structural_state
    UPDATE metabolic_state
    UPDATE signaling_state
    UPDATE cell_cycle_state
    UPDATE uncertainty
    PRESERVE provenance

  ON cell_state_transition:
    UPDATE gene_expression_state
    UPDATE metabolic_state
    UPDATE morphology
    UPDATE functional_state
    PRESERVE provenance

  ON new_experimental_evidence:
    UPDATE cell_claims
    UPDATE interaction_relationships
    UPDATE evidence_quality
    UPDATE confidence
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_CELL_ONTOLOGY
  reasoning_mode: CELL_ENTITY_STATE_RELATIONAL

  preserve:
    - typed_entities
    - cell_identity
    - cell_type
    - boundary_state
    - cellular_components
    - organelle_relationships
    - genome
    - gene_expression_state
    - metabolic_state
    - transport_state
    - signaling_state
    - cell_cycle_state
    - differentiation_state
    - evidence
    - uncertainty
    - confidence
    - provenance

  infer:
    - cell_type_dependencies
    - component_function_dependencies
    - genome_expression_dependencies
    - metabolic_dependencies
    - signaling_effects
    - cell_state_transitions
    - division_and_differentiation_state
    - homeostatic_and_stress_response
    - evidence_strength

  prohibit:
    - invented_cell_observations
    - fabricated_cell_components
    - assumed_cell_type_without_evidence
    - assumed_cell_state_without_evidence
    - unsupported_cellular_causality
    - missing_evidence_presented_as_established_fact

# FLOW HASH
FLOW_HASH_INPUT :=
  DOMAIN + ONTOLOGY + CORE_ENTITIES
  + IDENTITY_BOUNDARY_COMPONENTS
  + ORGANELLES_CYTOSKELETON_GENOME
  + METABOLISM_TRANSPORT_SIGNALING
  + CELL_STATE_CYCLE_DIVISION_DIFFERENTIATION
  + INTERACTIONS_HOMEOSTASIS_STRESS_DEATH
  + PROKARYOTIC_EUKARYOTIC
  + EVIDENCE_UNCERTAINTY_PROVENANCE
  + REASONING + INFERENCE_RULES
  + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE
  + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION

FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW