Cytoplasm Ontology

AI SEARCH FLOW ALGEBRA
CYTOPLASM ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

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

FLOW "CytoplasmOntology" v4.0
DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / CYTOPLASM
ONTOLOGY := CYTOPLASM_ONTOLOGY

CYTOPLASM := CYTOPLASMIC_IDENTITY + CYTOSOL + CELLULAR_COMPONENTS + ORGANELLES_WHERE_APPLICABLE + CYTOSKELETON + WATER + IONS + METABOLITES + PROTEINS + RNA + BIOCHEMICAL_REACTIONS + METABOLISM + DIFFUSION + INTRACELLULAR_TRANSPORT + MOLECULAR_CROWDING + VISCOSITY + PHASE_ORGANISATION + SIGNALING + SPATIAL_ORGANISATION + HOMEOSTASIS + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE := IDENTIFY_CYTOPLASM -> DISTINGUISH_CYTOSOL_FROM_SUSPENDED_COMPONENTS -> MAP_MOLECULAR_COMPOSITION -> MAP_ORGANELLES_AND_CYTOSKELETON -> MAP_BIOCHEMICAL_AND_METABOLIC_PROCESSES -> MAP_DIFFUSION_AND_INTRACELLULAR_TRANSPORT -> MAP_PHYSICAL_PROPERTIES_AND_CROWDING -> MAP_PHASE_ORGANISATION -> MAP_SIGNALING_AND_SPATIAL_GRADIENTS -> MAP_CYTOPLASMIC_HOMEOSTASIS -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY Cytoplasm
ENTITY Cytosol
ENTITY Cell
ENTITY Organelle
ENTITY Cytoskeleton
ENTITY Ribosome
ENTITY Vesicle
ENTITY Water
ENTITY Ion
ENTITY Metabolite
ENTITY Protein
ENTITY RNA
ENTITY Enzyme
ENTITY BiochemicalReaction
ENTITY MetabolicPathway
ENTITY Diffusion
ENTITY IntracellularTransport
ENTITY MolecularMotor
ENTITY MolecularCrowding
ENTITY Viscosity
ENTITY PH
ENTITY RedoxState
ENTITY OsmoticState
ENTITY BiomolecularCondensate
ENTITY PhaseSeparation
ENTITY Signal
ENTITY ConcentrationGradient
ENTITY Homeostasis
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# IDENTITY / CYTOSOL / COMPOSITION
Cytoplasm -> part_of -> Cell
Cytoplasm -> occupies -> CELL_INTERIOR_OUTSIDE_NUCLEAR_REGION_AS_DEFINED
Cytoplasm -> includes -> Cytosol + ORGANELLES_AND_STRUCTURES_WHERE_APPLICABLE + CYTOSKELETON + RIBOSOMES + VESICLES + DISSOLVED_AND_SUSPENDED_MOLECULES
Cytoplasm -> must_not_be_equated_with -> Cytosol

Cytosol -> fluid_phase_of -> Cytoplasm
Cytosol -> contains -> WATER + IONS + METABOLITES + PROTEINS + RNA + OTHER_SOLUBLE_COMPONENTS
Cytosol -> supports -> BIOCHEMICAL_REACTIONS + DIFFUSION + SIGNALING + METABOLIC_INTERACTIONS
CytosolicComposition -> varies_with -> CELL_TYPE + CELL_STATE + ENVIRONMENT + SUBCELLULAR_LOCATION

Water -> major_solvent_of -> Cytosol
Ion -> contributes_to -> IONIC_STRENGTH + OSMOTIC_STATE + ELECTROCHEMICAL_BALANCE + SIGNALING
Metabolite -> participates_in -> BIOCHEMICAL_REACTION
MetaboliteConcentration -> depends_on -> PRODUCTION + CONSUMPTION + TRANSPORT + COMPARTMENTAL_EXCHANGE

# RIBOSOMES / CYTOSKELETON / TRANSPORT
Ribosome -> present_in -> CYTOPLASM_OR_ASSOCIATED_COMPARTMENT_AS_APPLICABLE
Ribosome -> performs -> TRANSLATION
TRANSLATION_FLOW := MRNA -> RIBOSOME_BINDING -> POLYPEPTIDE_SYNTHESIS -> PROTEIN_FOLDING_AND_TARGETING

Cytoskeleton -> extends_through -> Cytoplasm
CYTOSKELETAL_COMPONENT := MICROTUBULE | ACTIN_FILAMENT | INTERMEDIATE_FILAMENT
Cytoskeleton -> organises -> CELL_SHAPE + ORGANELLE_POSITION + INTRACELLULAR_TRANSPORT + CELL_MIGRATION + CELL_DIVISION
CytoskeletalRemodelling -> changes -> CYTOPLASMIC_ORGANISATION

Organelle -> suspended_or_positioned_within -> Cytoplasm
Vesicle -> moves_through -> Cytoplasm

Diffusion -> moves -> MOLECULES -> according_to -> CONCENTRATION_AND_PHYSICAL_CONSTRAINTS
DiffusionRate -> influenced_by -> MOLECULAR_SIZE + TEMPERATURE + VISCOSITY + CROWDING + BINDING_INTERACTIONS

IntracellularTransport -> moves -> CARGO -> through -> Cytoplasm
TRANSPORT_MODE := DIFFUSIVE | MOTOR_DRIVEN | CYTOPLASMIC_FLOW | VESICULAR
MolecularMotor -> moves -> CARGO -> along -> CYTOSKELETAL_TRACK
DirectedTransport -> supports -> CELL_POLARITY + ORGANELLE_POSITIONING + LOCAL_PROTEIN_OR_RNA_DISTRIBUTION

# METABOLISM / PHYSICAL STATE / PHASE ORGANISATION
BiochemicalReaction -> may_occur_in -> Cytosol
Enzyme -> catalyses -> BiochemicalReaction
CYTOSOLIC_PROCESS := GLYCOLYSIS | BIOSYNTHETIC_REACTION | SIGNALING_REACTION | PROTEIN_MODIFICATION | REDOX_REACTION | OTHER_CYTOSOLIC_PROCESS
MetabolicPathway -> contains -> INTERCONNECTED_BIOCHEMICAL_REACTIONS
CytosolicMetabolism -> exchanges -> METABOLITES -> with -> ORGANELLES + EXTRACELLULAR_ENVIRONMENT_VIA_TRANSPORT
MetabolicFlux -> describes -> RATE_OF_MATERIAL_FLOW_THROUGH_PATHWAY
IF SubstrateAvailability changes THEN MetabolicFlux -> MAY_CHANGE

MolecularCrowding -> arises_from -> HIGH_MACROMOLECULAR_OCCUPANCY
MolecularCrowding -> influences -> DIFFUSION + BINDING + FOLDING + REACTION_KINETICS + PHASE_BEHAVIOUR
CytoplasmicViscosity -> influences -> MOLECULAR_MOTION + TRANSPORT + REACTION_DYNAMICS
CYTOPLASMIC_PHYSICAL_PROPERTY := VISCOSITY | ELASTICITY | DIFFUSIVITY | DENSITY | OSMOTIC_PRESSURE

PhaseSeparation -> may_form -> BiomolecularCondensate
BiomolecularCondensate -> concentrates -> SELECTED_MOLECULES
Condensate -> may_organise -> RNA_PROCESSING + SIGNALING + PROTEIN_REGULATION + STRESS_RESPONSE

# SPATIAL ORGANISATION / SIGNALING / HOMEOSTASIS
Cytoplasm -> spatially_organised -> TRUE
SpatialOrganisation -> includes -> ORGANELLE_POSITIONING + CYTOSKELETAL_ARCHITECTURE + MOLECULAR_GRADIENTS + LOCAL_TRANSLATION + SIGNALING_DOMAINS
LocalConcentration -> may_differ_from -> BULK_CYTOSOLIC_CONCENTRATION
SpatialOrganisation -> enables -> LOCAL_CONTROL_OF_CELLULAR_PROCESS

ConcentrationGradient -> represents -> SPATIAL_DIFFERENCE_IN_MOLECULAR_CONCENTRATION
Gradient -> may_drive -> DIFFUSION + SIGNALING + POLARITY + DEVELOPMENTAL_RESPONSE
GradientMaintenance -> may_require -> LOCAL_PRODUCTION + DEGRADATION + TRANSPORT + BINDING

Signal -> changes -> CYTOPLASMIC_SIGNALING_STATE
CYTOPLASMIC_SIGNALING := SECOND_MESSENGER_SIGNALING + PROTEIN_PHOSPHORYLATION + GTPASE_SIGNALING + CALCIUM_SIGNALING + OTHER_SIGNALING_NETWORK
SignalingState -> may_change -> GENE_EXPRESSION + METABOLISM + MOTILITY + SECRETION + CELL_FATE

CytosolicPH -> regulated_by -> BUFFERS + ION_TRANSPORT + METABOLIC_PROCESSES
RedoxState -> influenced_by -> METABOLISM + REACTIVE_OXYGEN_SPECIES + ANTIOXIDANT_SYSTEMS
OsmoticState -> depends_on -> SOLUTE_CONCENTRATION + WATER_BALANCE
EnergyState -> influences -> BIOSYNTHESIS + TRANSPORT + CYTOSKELETAL_ACTIVITY + SIGNALING

Homeostasis -> maintains -> CYTOPLASMIC_VARIABLE -> within -> FUNCTIONAL_RANGE
CYTOPLASMIC_VARIABLE := PH | ION_CONCENTRATION | OSMOTIC_STATE | REDOX_STATE | ENERGY_STATE | PROTEIN_QUALITY | METABOLITE_BALANCE
IF Stress exceeds_homeostatic_capacity THEN CellState -> MAY_CHANGE

# EVIDENCE / UNCERTAINTY / PROVENANCE
CytoplasmClaim -> supported_by -> Evidence
EVIDENCE_TYPE := MICROSCOPIC | BIOCHEMICAL | BIOPHYSICAL | MOLECULAR | IMAGING | METABOLOMIC | PROTEOMIC | FUNCTIONAL | COMPUTATIONAL
OBSERVATION_METHOD := LIVE_CELL_IMAGING | FLUORESCENCE_MICROSCOPY | ELECTRON_MICROSCOPY | FRAP | SINGLE_PARTICLE_TRACKING | BIOCHEMICAL_FRACTIONATION | MASS_SPECTROMETRY | SPECTROSCOPY | BIOSENSOR_MEASUREMENT
Evidence -> has -> SOURCE + METHOD + CELL_OR_SAMPLE + SUBCELLULAR_CONTEXT + CONDITION + QUALITY + UNCERTAINTY
Measurement -> may_describe -> CONCENTRATION + DIFFUSION + VISCOSITY + PH + REDOX_STATE + METABOLIC_FLUX + MOLECULAR_LOCALISATION

CYTOPLASM_UNCERTAINTY := MEASUREMENT_UNCERTAINTY + SPATIAL_HETEROGENEITY + TEMPORAL_VARIABILITY + CELL_TO_CELL_VARIABILITY + FRACTIONATION_ARTIFACT + MODEL_UNCERTAINTY
Uncertainty -> qualifies -> CytoplasmClaim + Concentration + DiffusionRate + MetabolicFlux + PhysicalProperty

Provenance -> records -> CELL_IDENTITY + CYTOPLASMIC_REGION + MOLECULE_OR_COMPONENT + METHOD + CONDITION + MEASUREMENT + TIME + VERSION
Cytoplasm -> linked_to -> Provenance

# REASONING / INFERENCE RULES
CYTOPLASM_REASONING := IDENTIFY_CYTOPLASM -> DISTINGUISH_CYTOSOL_AND_SUSPENDED_COMPONENTS -> MAP_MOLECULAR_COMPOSITION -> MAP_ORGANELLES_AND_CYTOSKELETON -> MAP_RIBOSOMES_AND_TRANSLATION -> MAP_DIFFUSION_AND_INTRACELLULAR_TRANSPORT -> MAP_BIOCHEMICAL_REACTIONS_AND_METABOLIC_FLUX -> MAP_CROWDING_AND_PHYSICAL_PROPERTIES -> MAP_PHASE_ORGANISATION -> MAP_SPATIAL_GRADIENTS -> MAP_SIGNALING -> MAP_PH_REDox_OSMOTIC_AND_ENERGY_STATE -> MAP_HOMEOSTASIS -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

IF CytosolicComposition changes THEN BiochemicalReactionRates -> MAY_CHANGE
IF MolecularCrowding increases THEN DiffusionAndBindingDynamics -> MAY_CHANGE
IF Cytoskeleton reorganises THEN OrganellePositionAndTransport -> MAY_CHANGE
IF CytosolicPH changes THEN EnzymeActivity -> MAY_CHANGE
IF RedoxState changes THEN ProteinAndMetabolicState -> MAY_CHANGE
IF OsmoticState changes THEN CellVolumeAndCrowding -> MAY_CHANGE
IF EnergyState decreases THEN EnergyDependentCytoplasmicProcesses -> MAY_DECREASE
IF ConcentrationGradient changes THEN LocalSignalingOrTransport -> MAY_CHANGE
IF Evidence insufficient THEN CytoplasmClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION part_of(Cytoplasm, Cell)
RELATION fluid_phase_of(Cytosol, Cytoplasm)
RELATION contains(Cytosol, Metabolite)
RELATION performs(Ribosome, Translation)
RELATION extends_through(Cytoskeleton, Cytoplasm)
RELATION positioned_within(Organelle, Cytoplasm)
RELATION moves_through(Vesicle, Cytoplasm)
RELATION moves(Diffusion, Molecule)
RELATION transports(IntracellularTransport, Cargo)
RELATION catalyses(Enzyme, BiochemicalReaction)
RELATION contains(MetabolicPathway, BiochemicalReaction)
RELATION influences(MolecularCrowding, Diffusion)
RELATION forms(PhaseSeparation, BiomolecularCondensate)
RELATION changes(Signal, CytoplasmicSignalingState)
RELATION maintains(Homeostasis, CytoplasmicVariable)
RELATION supports(Evidence, CytoplasmClaim)
RELATION records(Provenance, Cytoplasm)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "cytoplasm" ~= "cellular region containing cytosol and suspended cellular components outside the nuclear region as defined"
  "cytosol" ~= "aqueous soluble phase of the cytoplasm"
  "cytoplasmic transport" ~= "movement of molecules or cargo through cytoplasm"
  "molecular crowding" ~= "high macromolecular occupancy affecting molecular behaviour"
  "cytoplasmic viscosity" ~= "resistance of cytoplasmic material to molecular or bulk movement"
  "biomolecular condensate" ~= "concentrated non-membrane-bound molecular assembly formed through phase behaviour"
  "cytosolic metabolism" ~= "metabolic reactions occurring in the cytosolic compartment"
  "cytoplasmic homeostasis" ~= "maintenance of cytoplasmic physicochemical conditions within functional ranges"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  cytoplasm_cytosol_mapping: 0.99
  composition_mapping: 0.99
  cytoskeleton_transport_mapping: 0.99
  metabolism_mapping: 0.99
  physical_state_mapping: 0.99
  phase_organisation_mapping: 0.99
  signaling_homeostasis_mapping: 0.99
  evidence_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_cytoplasm_observation:
    MAP composition
    MAP cytoskeletal_state
    MAP organelle_positions
    MAP physical_state
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON metabolic_change:
    UPDATE metabolite_state
    UPDATE metabolic_flux
    UPDATE energy_state
    UPDATE redox_state
    PRESERVE provenance
  ON spatial_reorganisation:
    UPDATE gradients
    UPDATE transport_state
    UPDATE condensate_state
    UPDATE local_signaling
    PRESERVE provenance
  ON stress_event:
    UPDATE homeostatic_variables
    UPDATE protein_quality_state
    UPDATE uncertainty
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_CYTOPLASM_ONTOLOGY
  reasoning_mode: CYTOPLASMIC_SPATIAL_BIOCHEMICAL_RELATIONAL
  preserve: [typed_entities, cytoplasm_identity, cytosol_composition, organelle_positions, cytoskeletal_state, metabolite_state, transport_state, physical_properties, phase_organisation, signaling_state, homeostatic_state, evidence, uncertainty, confidence, provenance]
  infer: [composition_process_dependencies, diffusion_dependencies, transport_dependencies, crowding_effects, phase_behaviour, spatial_gradient_effects, signaling_effects, homeostatic_response, evidence_strength]
  prohibit: [equating_cytoplasm_with_cytosol, invented_cytoplasmic_observations, unsupported_condensate_assignment, assumed_metabolic_flux_without_evidence, unsupported_causality, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + IDENTITY_CYTOSOL_COMPOSITION + RIBOSOMES_CYTOSKELETON_TRANSPORT + METABOLISM_PHYSICAL_PHASE + SPATIAL_SIGNALING_HOMEOSTASIS + EVIDENCE_UNCERTAINTY_PROVENANCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW