Cell Biology Ontology

AI SEARCH FLOW ALGEBRA
CELL BIOLOGY ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

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

FLOW "CellBiologyOntology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / CELL_BIOLOGY_ONTOLOGY
ONTOLOGY := CELL_BIOLOGY_ONTOLOGY

CELL_BIOLOGY := CELL_IDENTITY + CELL_STRUCTURE + MEMBRANE + ORGANELLES + CYTOSKELETON + GENOME + GENE_EXPRESSION + PROTEOSTASIS + TRANSPORT + METABOLISM + BIOENERGETICS + SIGNALING + CELL_CYCLE + DIVISION + DIFFERENTIATION + CELL_FATE + ADHESION + MIGRATION + HOMEOSTASIS + STRESS + CELL_DEATH + NETWORKS + EVIDENCE + PROVENANCE

PURPOSE := IDENTIFY_CELL -> CLASSIFY_CELL_TYPE -> MAP_STRUCTURE -> MAP_MEMBRANES_AND_COMPARTMENTS -> MAP_ORGANELLE_FUNCTION -> MAP_CYTOSKELETON -> MAP_GENETIC_INFORMATION -> MAP_TRANSPORT_AND_TRAFFICKING -> MAP_METABOLISM_AND_ENERGY -> MAP_SIGNALING -> MAP_CELL_CYCLE_AND_DIVISION -> MAP_DIFFERENTIATION_AND_FATE -> MAP_HOMEOSTASIS_STRESS_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 Genome
ENTITY DNA
ENTITY RNA
ENTITY Gene
ENTITY Protein
ENTITY Receptor
ENTITY Transporter
ENTITY Signal
ENTITY MetabolicPathway
ENTITY CellSignaling
ENTITY CellCycle
ENTITY Mitosis
ENTITY Meiosis
ENTITY Cytokinesis
ENTITY Differentiation
ENTITY CellFate
ENTITY CellState
ENTITY CellAdhesion
ENTITY CellMigration
ENTITY CellularHomeostasis
ENTITY CellStress
ENTITY Apoptosis
ENTITY CellDeath
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# CELL IDENTITY AND STRUCTURE
Cell -> fundamental_unit_of -> CELLULAR_LIFE
CELL_TYPE := PROKARYOTIC | EUKARYOTIC
CellIdentity := SPECIES_OR_SOURCE + CELL_TYPE + DEVELOPMENTAL_CONTEXT + CELL_STATE
CELL_STRUCTURE := CELL_MEMBRANE + CYTOPLASM + GENETIC_MATERIAL + RIBOSOMES + ORGANELLES_WHERE_APPLICABLE + CYTOSKELETON_WHERE_APPLICABLE
CellStructure -> enables_or_constrains -> CellFunction
IF CellStructure changes THEN CellFunction -> MAY_CHANGE

# MEMBRANE AND COMPARTMENTS
CellMembrane -> separates -> INTRACELLULAR_ENVIRONMENT + EXTRACELLULAR_ENVIRONMENT
MEMBRANE_FUNCTION := SELECTIVE_BARRIER | TRANSPORT | SIGNAL_RECEPTION | CELL_ADHESION | ELECTROCHEMICAL_GRADIENT_MAINTENANCE
Compartmentalisation -> enables -> DISTINCT_LOCAL_CHEMICAL_ENVIRONMENTS + PROCESS_SPECIALISATION
IF CompartmentIntegrity fails THEN LocalCellularFunction -> MAY_CHANGE

# ORGANELLES AND CYTOSKELETON
Organelle -> part_of -> Cell
Nucleus -> contains -> CHROMOSOMAL_DNA_IN_EUKARYOTES
Mitochondrion -> participates_in -> ATP_PRODUCTION + METABOLISM + SIGNALING
Ribosome -> performs -> TRANSLATION
EndoplasmicReticulum -> participates_in -> PROTEIN_SYNTHESIS + PROTEIN_FOLDING + LIPID_SYNTHESIS
GolgiApparatus -> modifies_and_sorts -> PROTEINS + LIPIDS
Lysosome -> participates_in -> DEGRADATION + RECYCLING
Cytoskeleton -> organises -> CELL_SHAPE + INTRACELLULAR_TRANSPORT + CELL_MOTILITY + CELL_DIVISION
CYTOSKELETAL_COMPONENT := MICROTUBULE | ACTIN_FILAMENT | INTERMEDIATE_FILAMENT

# GENOME AND GENE EXPRESSION
Genome -> contains -> GENETIC_INFORMATION
Chromosome -> organises -> DNA
GENETIC_INFORMATION_FLOW := DNA -> TRANSCRIPTION -> RNA -> TRANSLATION -> PROTEIN
DNAReplication -> copies -> DNA -> before -> CELL_DIVISION_AS_APPLICABLE
IF ReplicationError persists THEN MutationRisk -> INCREASES
GeneExpression -> produces -> FUNCTIONAL_RNA | PROTEIN
GeneRegulation -> controls -> EXPRESSION_LEVEL + EXPRESSION_TIMING + EXPRESSION_LOCATION
IF GeneExpressionPattern changes THEN CellState -> MAY_CHANGE

# PROTEOSTASIS AND TRANSPORT
Proteostasis := PROTEIN_SYNTHESIS + FOLDING + TRAFFICKING + QUALITY_CONTROL + DEGRADATION
MisfoldedProtein -> may_trigger -> QUALITY_CONTROL + STRESS_RESPONSE
MEMBRANE_TRANSPORT := SIMPLE_DIFFUSION | FACILITATED_DIFFUSION | ACTIVE_TRANSPORT | ENDOCYTOSIS | EXOCYTOSIS
PassiveTransport -> follows -> ELECTROCHEMICAL_OR_CONCENTRATION_GRADIENT
ActiveTransport -> couples -> ENERGY -> to -> UPHILL_TRANSPORT
VESICULAR_TRANSPORT := CARGO_SELECTION -> VESICLE_BUDDING -> TRANSPORT -> TARGET_RECOGNITION -> MEMBRANE_FUSION

# METABOLISM AND BIOENERGETICS
CELL_METABOLISM := CATABOLISM + ANABOLISM + ENERGY_TRANSFER + BIOSYNTHESIS
MetabolicPathway -> contains -> INTERCONNECTED_BIOCHEMICAL_REACTIONS
Enzyme -> catalyses -> BIOCHEMICAL_REACTION
CELLULAR_WORK := CHEMICAL_WORK | TRANSPORT_WORK | MECHANICAL_WORK | INFORMATIONAL_AND_REGULATORY_WORK
ATP -> commonly_couples -> ENERGY_RELEASING_PROCESS + ENERGY_REQUIRING_PROCESS
EnergyCharge -> influences -> METABOLIC_AND_SIGNALING_STATE

# SIGNALING
CellSignaling -> communicates -> INFORMATION
SIGNALING_FLOW := SIGNAL -> RECEPTOR -> SIGNAL_TRANSDUCTION -> EFFECTOR -> CELLULAR_RESPONSE
CELLULAR_RESPONSE := GENE_EXPRESSION | METABOLIC_CHANGE | SECRETION | MOTILITY | DIVISION | DIFFERENTIATION | SURVIVAL | CELL_DEATH
SIGNALING_MODE := AUTOCRINE | PARACRINE | ENDOCRINE | SYNAPTIC | CONTACT_DEPENDENT
SignalResponse -> depends_on -> RECEPTOR_EXPRESSION + SIGNAL_CONCENTRATION + CELL_STATE + NETWORK_CONTEXT

# CELL CYCLE AND DIVISION
CellCycle -> coordinates -> GROWTH + DNA_REPLICATION + CHROMOSOME_SEGREGATION + CELL_DIVISION
CELL_CYCLE_PHASE := G1 | S | G2 | M | G0_AS_APPLICABLE
Checkpoint -> assesses -> DNA_INTEGRITY + REPLICATION_COMPLETION + CELL_SIZE_OR_STATE + SPINDLE_ATTACHMENT_AS_APPLICABLE
IF CheckpointRequirement not_met THEN CellCycleProgression -> DELAY_OR_ARREST
Mitosis -> segregates -> DUPLICATED_CHROMOSOMES -> into -> DAUGHTER_NUCLEI
Cytokinesis -> partitions -> CELL_CONTENT -> into -> DAUGHTER_CELLS
Meiosis -> reduces -> CHROMOSOME_SET_NUMBER -> for -> SEXUAL_REPRODUCTION_AS_APPLICABLE
Meiosis -> contributes_to -> GENETIC_VARIATION

# DIFFERENTIATION AND CELL STATE
Differentiation -> transforms -> CELL_STATE -> toward -> SPECIALISED_CELL_STATE
Differentiation -> involves -> GENE_REGULATORY_CHANGE + EPIGENETIC_CHANGE + SIGNALING + STRUCTURAL_CHANGE
CellFate -> describes -> DEVELOPMENTAL_DESTINATION_OR_STATE
CellState := GENE_EXPRESSION_STATE + EPIGENETIC_STATE + PROTEIN_STATE + METABOLIC_STATE + MORPHOLOGY + SIGNALING_STATE + CELL_CYCLE_STATE
CELL_STATE_TYPE := PROLIFERATING | QUIESCENT | DIFFERENTIATING | DIFFERENTIATED | STRESSED | SENESCENT | DYING

# ADHESION MIGRATION AND POLARITY
CellAdhesion -> connects -> 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 -> REAR_DETACHMENT -> TRANSLOCATION
CellPolarity -> creates -> ASYMMETRIC_CELLULAR_ORGANISATION
Polarity -> influences -> TRANSPORT + MIGRATION + DIVISION + SIGNALING

# HOMEOSTASIS STRESS AND DEATH
CellularHomeostasis -> maintains -> INTERNAL_VARIABLES -> within -> FUNCTIONAL_RANGE
HOMEOSTATIC_VARIABLE := ION_CONCENTRATION | PH | OSMOTIC_STATE | REDOX_STATE | ENERGY_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
CellDeath -> may_contribute_to -> DEVELOPMENT + TISSUE_HOMEOSTASIS + DAMAGE_RESPONSE

# CELLULAR NETWORKS
CELLULAR_NETWORK := GENE_REGULATORY_NETWORK | SIGNALING_NETWORK | METABOLIC_NETWORK | PROTEIN_INTERACTION_NETWORK
Node -> represents -> CELLULAR_COMPONENT_OR_STATE
Edge -> represents -> INTERACTION + REGULATION + TRANSFORMATION
NetworkState -> influences -> CELL_BEHAVIOUR

# PROKARYOTIC AND EUKARYOTIC CELLS
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 -> separates -> CELLULAR_PROCESSES -> into -> ORGANELLES_AND_REGIONS

# EVIDENCE UNCERTAINTY AND 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_GENOME_AND_GENE_EXPRESSION -> MAP_PROTEOSTASIS -> MAP_MEMBRANE_AND_VESICULAR_TRANSPORT -> MAP_METABOLISM_AND_BIOENERGETICS -> MAP_SIGNALING_AND_COMMUNICATION -> MAP_CELL_CYCLE_AND_DIVISION -> MAP_DIFFERENTIATION_AND_CELL_FATE -> MAP_CELL_STATE -> MAP_ADHESION_MIGRATION_AND_POLARITY -> MAP_HOMEOSTASIS_AND_STRESS -> MAP_CELL_DEATH -> 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 contains(MetabolicPathway, BiochemicalReaction)
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, InternalVariable)
RELATION terminates(CellDeath, CellularLivingState)
RELATION supports(Evidence, CellClaim)
RELATION records(Provenance, Cell)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "cell biology ontology" ~= "formal ontology of cellular entities structures and processes"
  "cell membrane" ~= "plasma membrane"
  "cell signaling" ~= "cellular signal transduction"
  "gene expression" ~= "production of functional RNA or protein from genetic information"
  "proteostasis" ~= "cellular protein homeostasis"
  "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"
  "apoptosis" ~= "regulated apoptotic cell death"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  cell_identity_structure_mapping: 0.99
  membrane_organelle_mapping: 0.99
  genome_expression_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 genome_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
  ON new_experimental_evidence:
    UPDATE interaction_relationships
    UPDATE process_relationships
    UPDATE evidence_quality
    UPDATE confidence
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_CELL_BIOLOGY_ONTOLOGY
  reasoning_mode: CELLULAR_ENTITY_PROCESS_RELATIONAL
  preserve: [typed_entities, cell_identity, cell_type, cell_state, membrane_state, organelle_relationships, cytoskeletal_relationships, genome, gene_expression_state, 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_IDENTITY_STRUCTURE + MEMBRANE_COMPARTMENTS + ORGANELLES_CYTOSKELETON + GENOME_GENE_EXPRESSION + PROTEOSTASIS_TRANSPORT + METABOLISM_BIOENERGETICS + SIGNALING_COMMUNICATION + CELL_CYCLE_DIVISION + DIFFERENTIATION_CELL_STATE + ADHESION_MIGRATION_POLARITY + HOMEOSTASIS_STRESS_DEATH + CELLULAR_NETWORKS + 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