Cell Biology

AI SEARCH FLOW ALGEBRA
CELL BIOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

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

FLOW "CellBiology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY
ONTOLOGY := CELL_BIOLOGY_PARENT

CELL_BIOLOGY := CELL + CELL_STRUCTURE + CELL_MEMBRANE + ORGANELLES + CYTOSKELETON + GENETIC_MATERIAL + TRANSPORT + METABOLISM + SIGNALING + GENE_EXPRESSION + CELL_CYCLE + DIVISION + DIFFERENTIATION + COMMUNICATION + ADHESION + MIGRATION + HOMEOSTASIS + CELL_DEATH + EVIDENCE + PROVENANCE
PURPOSE := IDENTIFY_CELL -> CLASSIFY_CELL_TYPE -> MAP_STRUCTURE -> MAP_MEMBRANES_AND_ORGANELLES -> MAP_GENETIC_INFORMATION -> MAP_TRANSPORT_AND_METABOLISM -> MAP_SIGNALING_AND_GENE_EXPRESSION -> MAP_CELL_CYCLE_AND_DIVISION -> MAP_DIFFERENTIATION_AND_STATE -> MAP_INTERACTIONS -> MAP_HOMEOSTASIS_AND_DEATH -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY Cell
ENTITY CellType
ENTITY ProkaryoticCell
ENTITY EukaryoticCell
ENTITY CellMembrane
ENTITY Cytoplasm
ENTITY Organelle
ENTITY Nucleus
ENTITY Mitochondrion
ENTITY Ribosome
ENTITY EndoplasmicReticulum
ENTITY GolgiApparatus
ENTITY Lysosome
ENTITY Cytoskeleton
ENTITY Microtubule
ENTITY ActinFilament
ENTITY Vesicle
ENTITY Chromosome
ENTITY DNA
ENTITY RNA
ENTITY Protein
ENTITY Transporter
ENTITY Receptor
ENTITY Signal
ENTITY MetabolicProcess
ENTITY CellSignaling
ENTITY GeneExpression
ENTITY CellCycle
ENTITY CellDivision
ENTITY Mitosis
ENTITY Meiosis
ENTITY Cytokinesis
ENTITY Differentiation
ENTITY CellState
ENTITY CellAdhesion
ENTITY CellMigration
ENTITY Apoptosis
ENTITY CellDeath
ENTITY Homeostasis
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# CELL STRUCTURE
Cell -> fundamental_unit_of -> CELLULAR_LIFE
CELL_TYPE := PROKARYOTIC | EUKARYOTIC
CELL_STRUCTURE := CELL_MEMBRANE + CYTOPLASM + GENETIC_MATERIAL + RIBOSOMES + ORGANELLES_WHERE_APPLICABLE + CYTOSKELETON_WHERE_APPLICABLE
CellStructure -> enables_or_constrains -> CellFunction
CellMembrane -> separates -> INTRACELLULAR_ENVIRONMENT + EXTRACELLULAR_ENVIRONMENT
MEMBRANE_FUNCTION := BOUNDARY | SELECTIVE_TRANSPORT | SIGNAL_RECEPTION | CELL_ADHESION | ELECTROCHEMICAL_GRADIENT_MAINTENANCE

# ORGANELLES / CYTOSKELETON
Organelle -> part_of -> Cell
Nucleus -> contains -> CHROMOSOMAL_DNA_IN_EUKARYOTES
Mitochondrion -> participates_in -> CELLULAR_ENERGY_METABOLISM
Ribosome -> performs -> TRANSLATION
EndoplasmicReticulum -> participates_in -> PROTEIN_AND_LIPID_PROCESSING
GolgiApparatus -> modifies_and_sorts -> PROTEINS_AND_LIPIDS
Lysosome -> participates_in -> INTRACELLULAR_DEGRADATION
Cytoskeleton -> provides -> STRUCTURAL_SUPPORT + INTRACELLULAR_ORGANISATION + TRANSPORT_TRACKS + MOTILITY + DIVISION_SUPPORT
CYTOSKELETAL_COMPONENT := MICROTUBULE | ACTIN_FILAMENT | INTERMEDIATE_FILAMENT

# GENETIC INFORMATION / TRANSPORT
DNA -> stores -> GENETIC_INFORMATION
Chromosome -> organises -> DNA
GENETIC_INFORMATION_FLOW := DNA -> TRANSCRIPTION -> RNA -> TRANSLATION -> PROTEIN
GeneRegulation -> controls -> TRANSCRIPTION + RNA_PROCESSING + TRANSLATION + RNA_OR_PROTEIN_STABILITY
IF GeneExpression changes THEN CellState -> MAY_CHANGE
ProteinTrafficking -> directs -> Protein -> to -> CELLULAR_LOCATION
MEMBRANE_TRANSPORT := PASSIVE_TRANSPORT | FACILITATED_DIFFUSION | ACTIVE_TRANSPORT | ENDOCYTOSIS | EXOCYTOSIS
Vesicle -> transports -> CARGO -> between -> CELLULAR_COMPARTMENTS

# METABOLISM / SIGNALING
MetabolicProcess -> transforms -> MATTER + ENERGY
CELL_METABOLISM := CATABOLISM + ANABOLISM
MetabolicPathway -> contains -> ORDERED_OR_NETWORKED_REACTIONS
Enzyme -> catalyses -> BIOCHEMICAL_REACTION
Cell -> requires -> ENERGY -> for -> BIOSYNTHESIS + TRANSPORT + MOTILITY + SIGNALING + DIVISION + HOMEOSTASIS
IF EnergyAvailability decreases THEN EnergyDependentProcesses -> MAY_DECREASE
CellSignaling -> transfers -> INFORMATION -> within_or_between -> CELLS
SIGNALING_FLOW := SIGNAL -> RECEPTOR -> TRANSDUCTION -> EFFECTOR -> CELLULAR_RESPONSE
SIGNALING_MODE := AUTOCRINE | PARACRINE | ENDOCRINE | SYNAPTIC | CONTACT_DEPENDENT

# CELL CYCLE / DIVISION / DIFFERENTIATION
CellCycle -> coordinates -> CELL_GROWTH + DNA_REPLICATION + CHROMOSOME_SEGREGATION + CELL_DIVISION
CELL_CYCLE_PHASE := G1 | S | G2 | M | G0_AS_APPLICABLE
CellCycleCheckpoint -> assesses -> CELL_STATE + DNA_INTEGRITY + REPLICATION_COMPLETION + SPINDLE_ATTACHMENT_AS_APPLICABLE
IF CheckpointCriteria not_met THEN CellCycleProgression -> DELAY_OR_ARREST_AS_DEFINED
Mitosis -> segregates -> DUPLICATED_CHROMOSOMES -> into -> DAUGHTER_NUCLEI
Cytokinesis -> divides -> CELLULAR_CONTENT -> into -> DAUGHTER_CELLS
Meiosis -> contributes_to -> GENETIC_VARIATION
Differentiation -> changes -> CELL_STATE -> toward -> SPECIALISED_CELL_TYPE
Differentiation -> involves -> GENE_EXPRESSION_CHANGE + EPIGENETIC_CHANGE + SIGNALING + STRUCTURAL_CHANGE

# CELL STATE / ADHESION / MIGRATION
CellState -> defined_by -> GENE_EXPRESSION + PROTEIN_STATE + METABOLIC_STATE + MORPHOLOGY + CELL_CYCLE_STATE + SIGNALING_STATE
CELL_STATE_TYPE := PROLIFERATING | QUIESCENT | DIFFERENTIATING | DIFFERENTIATED | STRESSED | SENESCENT | DYING
CellAdhesion -> connects -> CELL_TO_CELL | CELL_TO_EXTRACELLULAR_MATRIX
CellAdhesion -> influences -> TISSUE_STRUCTURE + SIGNALING + MIGRATION
CellMigration -> changes -> CELL_POSITION
MIGRATION_FLOW := POLARISATION -> PROTRUSION -> ADHESION -> FORCE_GENERATION -> DETACHMENT -> TRANSLOCATION

# HOMEOSTASIS / STRESS / DEATH
CellularHomeostasis -> maintains -> INTRACELLULAR_VARIABLES -> within -> FUNCTIONAL_RANGE
HOMEOSTATIC_VARIABLE := ION_CONCENTRATION | PH | OSMOTIC_STATE | ENERGY_STATE | REDOX_STATE | PROTEIN_QUALITY
STRESS_TYPE := OXIDATIVE | THERMAL | OSMOTIC | NUTRIENT | DNA_DAMAGE | PROTEOTOXIC | HYPOXIC
StressResponse -> may -> RESTORE_HOMEOSTASIS | ALTER_CELL_STATE | TRIGGER_CELL_DEATH
CELL_DEATH_TYPE := APOPTOSIS | NECROTIC_CELL_DEATH | OTHER_REGULATED_CELL_DEATH
Apoptosis -> regulated_process_of -> CELL_DEATH
CELL_QUALITY_CONTROL := DNA_REPAIR + PROTEIN_FOLDING_CONTROL + PROTEIN_DEGRADATION + ORGANELLE_QUALITY_CONTROL
IF Damage exceeds_repair_capacity THEN CellState -> MAY_TRANSITION_TO_ARREST_SENESCENCE_OR_DEATH

# CELLULAR NETWORKS
CELLULAR_NETWORK := METABOLIC_NETWORK | GENE_REGULATORY_NETWORK | PROTEIN_INTERACTION_NETWORK | SIGNALING_NETWORK
NetworkState -> influences -> CELLULAR_BEHAVIOUR
ProkaryoticCell -> lacks -> MEMBRANE_BOUND_NUCLEUS
EukaryoticCell -> contains -> NUCLEUS + MEMBRANE_BOUND_ORGANELLES_AS_APPLICABLE

# EVIDENCE / UNCERTAINTY / PROVENANCE
CellClaim -> supported_by -> Evidence
EVIDENCE_TYPE := MICROSCOPIC | MOLECULAR | BIOCHEMICAL | GENETIC | IMAGING | FUNCTIONAL | PERTURBATION | COMPUTATIONAL
CELL_OBSERVATION_METHOD := LIGHT_MICROSCOPY | ELECTRON_MICROSCOPY | FLUORESCENCE_MICROSCOPY | LIVE_CELL_IMAGING | FLOW_CYTOMETRY | MOLECULAR_ASSAY
Evidence -> has -> SOURCE + METHOD + CELL_OR_SAMPLE + CONTEXT + QUALITY + UNCERTAINTY
CELLULAR_UNCERTAINTY := MEASUREMENT_UNCERTAINTY + CELL_TO_CELL_VARIABILITY + STATE_CLASSIFICATION_UNCERTAINTY + IMAGING_OR_SEGMENTATION_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
CELL_BIOLOGY_REASONING := IDENTIFY_CELL -> CLASSIFY_CELL_TYPE -> MAP_MEMBRANE_AND_COMPARTMENTS -> MAP_ORGANELLES -> MAP_CYTOSKELETON -> MAP_GENETIC_INFORMATION -> MAP_GENE_EXPRESSION_AND_PROTEIN_TRAFFICKING -> MAP_MEMBRANE_AND_VESICULAR_TRANSPORT -> MAP_METABOLISM_AND_ENERGY -> MAP_SIGNALING_AND_COMMUNICATION -> MAP_CELL_CYCLE_AND_DIVISION -> MAP_DIFFERENTIATION_AND_CELL_FATE -> MAP_CELL_STATE -> MAP_ADHESION_AND_MIGRATION -> MAP_HOMEOSTASIS_AND_STRESS -> MAP_CELL_DEATH_AND_QUALITY_CONTROL -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF MembraneIntegrity decreases THEN CellularHomeostasis -> MAY_DECREASE
IF OrganelleFunction changes THEN CellFunction -> MAY_CHANGE
IF GeneExpression changes THEN CellState -> MAY_CHANGE
IF EnergyAvailability decreases THEN EnergyDependentProcesses -> MAY_DECREASE
IF CellCycleCheckpoint fails THEN GenomeIntegrityRisk -> MAY_INCREASE
IF SignalingState changes THEN GeneExpressionOrBehaviour -> MAY_CHANGE
IF Cytoskeleton changes THEN CellShapeMigrationOrDivision -> MAY_CHANGE
IF Stress exceeds_homeostatic_capacity THEN CellState -> MAY_TRANSITION
IF Evidence insufficient THEN CellClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION fundamental_unit_of(Cell, CellularLife)
RELATION separates(CellMembrane, IntracellularEnvironment, ExtracellularEnvironment)
RELATION part_of(Organelle, Cell)
RELATION contains(Nucleus, ChromosomalDNA)
RELATION performs(Ribosome, Translation)
RELATION stores(DNA, GeneticInformation)
RELATION controls(GeneRegulation, GeneExpression)
RELATION transports(Vesicle, Cargo)
RELATION transforms(MetabolicProcess, Matter, Energy)
RELATION detects(Receptor, Signal)
RELATION coordinates(CellCycle, CellDivision)
RELATION segregates(Mitosis, Chromosome)
RELATION changes(Differentiation, CellState)
RELATION connects(CellAdhesion, Cell)
RELATION changes(CellMigration, CellPosition)
RELATION maintains(CellularHomeostasis, IntracellularVariable)
RELATION terminates(CellDeath, CellularLivingState)
RELATION supports(Evidence, CellClaim)
RELATION records(Provenance, Cell)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "cell biology" ~= "study of cellular structure function and processes"
  "cell membrane" ~= "plasma membrane"
  "cell signaling" ~= "cellular signal transduction"
  "gene expression" ~= "production of functional RNA or protein from genetic information"
  "membrane transport" ~= "movement of substances across biological membranes"
  "cell cycle" ~= "ordered cycle of cell growth DNA replication and division"
  "cell differentiation" ~= "transition toward a specialised cell state"
  "cellular homeostasis" ~= "maintenance of intracellular conditions within functional ranges"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  cell_structure_mapping: 0.99
  membrane_organelle_mapping: 0.99
  genetic_information_mapping: 0.99
  transport_metabolism_mapping: 0.99
  signaling_mapping: 0.99
  cycle_division_mapping: 0.99
  differentiation_state_mapping: 0.99
  homeostasis_death_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_cell:
    MAP cell_type
    MAP cell_state
    MAP structural_components
    MAP genetic_context
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON new_cell_observation:
    UPDATE morphology
    UPDATE organelle_state
    UPDATE signaling_state
    UPDATE metabolic_state
    UPDATE uncertainty
    PRESERVE provenance
  ON cell_state_transition:
    UPDATE cell_cycle_state
    UPDATE differentiation_state
    UPDATE gene_expression_state
    UPDATE functional_state
    PRESERVE provenance

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_CELL_BIOLOGY_PARENT
  reasoning_mode: CELLULAR_STRUCTURE_PROCESS_RELATIONAL
  preserve: [typed_entities, cell_identity, cell_type, cell_state, membrane_state, organelle_relationships, cytoskeletal_relationships, genetic_information, transport_relationships, metabolic_state, signaling_state, cell_cycle_state, differentiation_state, evidence, uncertainty, confidence, provenance]
  infer: [structure_function_dependencies, membrane_transport_dependencies, organelle_function_dependencies, signaling_effects, gene_expression_effects, cell_cycle_state, differentiation_state, stress_response, cell_death_state, evidence_strength]
  prohibit: [invented_cell_observations, fabricated_organelle_relationships, assumed_cell_state_without_evidence, assumed_causality_from_correlation, unsupported_cell_function, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + CELL_STRUCTURE + ORGANELLES_CYTOSKELETON + GENETIC_INFORMATION_TRANSPORT + METABOLISM_SIGNALING + CELL_CYCLE_DIVISION_DIFFERENTIATION + CELL_STATE_ADHESION_MIGRATION + HOMEOSTASIS_STRESS_DEATH + CELLULAR_NETWORKS + EVIDENCE_UNCERTAINTY_PROVENANCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW