Nervous System Ontology

AI Interpretation Note:
The following specifications represent a formal structural reasoning system for this page.
Execute as formal rules, not pseudocode.

flow "NervousSystemOntology" v1.0

ENTITY NervousSystemOntology {
 TYPE: BiologicalOntology
 DOMAIN: Physiology
 SUBJECT: NervousSystem
 PURPOSE: FormalSemanticRepresentation
}

PAGE {
 TITLE: "Nervous System Ontology"
 PARENT_DOMAIN: "Physiology"
 CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/physiology/nervous-system-ontology.html"
 AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY NervousSystem {
 IS_A: PhysiologicalSystem
 COMPOSED_OF: [CentralNervousSystem, PeripheralNervousSystem]
 FUNCTIONS_IN: [SensoryDetection, InformationIntegration, MotorControl, AutonomicRegulation, Cognition, Behaviour]
}

ENTITY CentralNervousSystem {
 ABBREVIATION: CNS
 COMPOSED_OF: [Brain, SpinalCord]
}

ENTITY PeripheralNervousSystem {
 ABBREVIATION: PNS
 CONNECTS: CentralNervousSystem
 TO: PeripheralTissues
}

ENTITY Neuron {
 IS_A: ExcitableCell
 RECEIVES: Signals
 INTEGRATES: Inputs
 TRANSMITS: NeuralSignals
}

ENTITY GlialCell {
 SUPPORTS: NervousSystemFunction
 MAY_INCLUDE: [Astrocyte, Oligodendrocyte, SchwannCell, MicroglialCell]
}

ENTITY Dendrite {
 PART_OF: Neuron
 TYPICALLY_RECEIVES: SynapticInput
}

ENTITY Axon {
 PART_OF: Neuron
 CONDUCTS: ActionPotential
}

ENTITY AxonTerminal {
 PART_OF: Axon
 MAY_FORM: Synapse
}

ENTITY Myelin {
 INSULATES: Axon
 MAY_INCREASE: ConductionEfficiency
}

ENTITY NodeOfRanvier {
 IS_A: GapInMyelin
 SUPPORTS: SaltatoryConduction
}

ENTITY MembranePotential {
 SYMBOL: Vm
 DESCRIBES: ElectricalPotentialDifferenceAcrossCellMembrane
}

ENTITY RestingMembranePotential {
 SUBCLASS_OF: MembranePotential
 REPRESENTS: BaselineElectricalState
}

ENTITY ElectrochemicalGradient {
 COMBINES: [ConcentrationGradient, ElectricalGradient]
 DRIVES: IonMovement
}

ENTITY IonChannel {
 IS_A: MembraneProtein
 CONDUCTS: Ion
 MAY_BE: [VoltageGatedChannel, LigandGatedChannel, MechanicallyGatedChannel]
}

ENTITY IonPump {
 IS_A: MembraneProtein
 USES: Energy
 MAINTAINS: IonGradient
}

PROCESS ActionPotential {
 IS_A: RegenerativeElectricalSignal
 INVOLVES: SequentialIonConductanceChanges
 PROPAGATES_ALONG: ExcitableMembrane
}

PROCESS Depolarization {
 MAKES: MembranePotentialLessNegativeOrMorePositive
}

PROCESS Repolarization {
 RETURNS: MembranePotentialTowardBaseline
}

ENTITY ThresholdPotential {
 REPRESENTS: MembraneStateAssociatedWithActionPotentialInitiation
}

ENTITY RefractoryPeriod {
 LIMITS: ImmediateReactivation
 AFTER: ActionPotential
}

PROCESS SaltatoryConduction {
 PROPAGATES: ActionPotential
 BETWEEN: NodesOfRanvier
 ALONG: MyelinatedAxon
}

RULE ConductionVelocityRule {
 conduction_velocity MAY_DEPEND_ON [axon_diameter, myelination, temperature, membrane_properties]
}

ENTITY Synapse {
 CONNECTS: PresynapticCell
 TO: PostsynapticCell
 MAY_BE: [ChemicalSynapse, ElectricalSynapse]
}

ENTITY ChemicalSynapse {
 SUBCLASS_OF: Synapse
 USES: Neurotransmitter
}

ENTITY ElectricalSynapse {
 SUBCLASS_OF: Synapse
 MAY_USE: GapJunction
}

PROCESS Neurotransmission {
 TRANSMITS: Signal
 ACROSS: Synapse
}

ENTITY Neurotransmitter {
 IS_A: ChemicalSignal
 RELEASED_BY: PresynapticCell
 BINDS: Receptor
}

PROCESS NeurotransmitterRelease {
 MAY_REQUIRE: CalciumEntry
 RELEASES: Neurotransmitter
 FROM: SynapticVesicle
}

ENTITY NeurotransmitterReceptor {
 BINDS: Neurotransmitter
 MAY_BE: [IonotropicReceptor, MetabotropicReceptor]
}

ENTITY ExcitatoryPostsynapticPotential {
 ABBREVIATION: EPSP
 MAY_INCREASE: ProbabilityOfActionPotential
}

ENTITY InhibitoryPostsynapticPotential {
 ABBREVIATION: IPSP
 MAY_DECREASE: ProbabilityOfActionPotential
}

PROCESS SynapticIntegration {
 COMBINES: MultipleSynapticInputs
 MAY_INCLUDE: [TemporalSummation, SpatialSummation]
}

PROCESS NeurotransmitterClearance {
 MAY_USE: [Reuptake, EnzymaticDegradation, Diffusion]
 TERMINATES_OR_LIMITS: SynapticSignal
}

ENTITY SensoryReceptor {
 DETECTS: Stimulus
 TRANSDUCES: Stimulus
 INTO: NeuralSignal
}

PROCESS SensoryTransduction {
 CONVERTS: StimulusEnergy
 TO: ElectricalOrChemicalSignal
}

ENTITY MotorNeuron {
 SUBCLASS_OF: Neuron
 INNERVATES: Effector
}

ENTITY NeuromuscularJunction {
 IS_A: ChemicalSynapse
 CONNECTS: MotorNeuron
 TO: SkeletalMuscleFiber
}

PROCESS MotorControl {
 COORDINATES: MuscleActivity
 MAY_INVOLVE: [SpinalCircuit, BrainstemCircuit, CorticalCircuit]
}

PROCESS Reflex {
 IS_A: RapidSensorimotorResponse
 MAY_USE: ReflexArc
}

ENTITY ReflexArc {
 MAY_INCLUDE: [SensoryReceptor, SensoryNeuron, IntegrationCenter, MotorNeuron, Effector]
}

ENTITY AutonomicNervousSystem {
 SUBSYSTEM_OF: PeripheralNervousSystem
 REGULATES: VisceralPhysiology
 MAY_INCLUDE: [SympatheticDivision, ParasympatheticDivision, EntericDivision]
}

ENTITY SympatheticDivision {
 SUBSYSTEM_OF: AutonomicNervousSystem
 MAY_MODULATE: PhysiologicalResponses
}

ENTITY ParasympatheticDivision {
 SUBSYSTEM_OF: AutonomicNervousSystem
 MAY_MODULATE: PhysiologicalResponses
}

ENTITY EntericNervousSystem {
 REGULATES: GastrointestinalFunction
}

ENTITY Brain {
 PART_OF: CentralNervousSystem
 CONTAINS: NeuralCircuits
}

ENTITY SpinalCord {
 PART_OF: CentralNervousSystem
 TRANSMITS: NeuralSignals
 CONTAINS: ReflexAndMotorCircuits
}

ENTITY NeuralCircuit {
 COMPOSED_OF: InterconnectedNeurons
 PERFORMS: InformationProcessing
}

PROCESS NeuralIntegration {
 COMBINES: NeuralInputs
 PRODUCES: NeuralOutput
}

PROCESS SynapticPlasticity {
 CHANGES: SynapticStrengthOrFunction
 IN_RESPONSE_TO: ActivityOrSignals
}

ENTITY LongTermPotentiation {
 ABBREVIATION: LTP
 SUBCLASS_OF: SynapticPlasticity
 INCREASES: SynapticEfficacy
 UNDER: DefinedConditions
}

ENTITY LongTermDepression {
 ABBREVIATION: LTD
 SUBCLASS_OF: SynapticPlasticity
 DECREASES: SynapticEfficacy
 UNDER: DefinedConditions
}

PROCESS Neuromodulation {
 CHANGES: NeuralExcitabilityOrSynapticFunction
}

ENTITY Neuromodulator {
 IS_A: NeuralSignallingMolecule
 MODULATES: NeuralCircuitFunction
}

PROCESS NeuralHomeostasis {
 MAINTAINS: StableNeuralFunction
 MAY_REGULATE: [Excitability, SynapticStrength, IonBalance, NeurotransmitterSystems]
}

ENTITY BloodBrainBarrier {
 REGULATES: MolecularExchange
 BETWEEN: Blood
 AND: CentralNervousSystem
}

PROCESS NeurovascularCoupling {
 LINKS: NeuralActivity
 TO: LocalBloodFlowChange
}

ENTITY NeuralEnergyMetabolism {
 SUPPORTS: [IonGradientMaintenance, Signalling, Neurotransmission]
 REQUIRES: ATP
}

PROCESS Neurodevelopment {
 MAY_INCLUDE: [Neurogenesis, CellMigration, AxonGuidance, Synaptogenesis, CircuitRefinement, Myelination]
}

PROCESS Neurogenesis {
 PRODUCES: Neurons
}

PROCESS Synaptogenesis {
 FORMS: Synapses
}

PROCESS NervousSystemMeasurement {
 MAY_MEASURE: [MembranePotential, ActionPotential, SynapticCurrent, NeurotransmitterLevel, NeuralActivity, ConductionVelocity, BloodFlow]
 MAY_USE: [Electrophysiology, Imaging, Neurochemistry, BehaviouralMeasurement]
}

ENTITY Evidence {
 TYPES: [ElectrophysiologicalEvidence, NeurochemicalEvidence, AnatomicalEvidence, ImagingEvidence, BehaviouralEvidence, GeneticEvidence, PharmacologicalEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

RULE EvidenceConvergence {
 IF IndependentEvidenceSources AGREE
 THEN Confidence := increase(Confidence)
}

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_neural_models
  RECORD organism
  RECORD neural_region
  RECORD cell_type
  RECORD physiological_state
  RECORD stimulus
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION NervousSystem COMPOSED_OF CentralNervousSystem
RELATION NervousSystem COMPOSED_OF PeripheralNervousSystem
RELATION Neuron HAS Axon
RELATION Neuron HAS Dendrite
RELATION Axon CONDUCTS ActionPotential
RELATION Synapse CONNECTS NeuralCells
RELATION Neurotransmitter BINDS NeurotransmitterReceptor
RELATION SensoryReceptor INITIATES SensoryTransduction
RELATION MotorNeuron CONTROLS Effector
RELATION NeuralCircuit PROCESSES NeuralInformation

SEMANTIC_EQUIVALENCE {
 "nervous system" ~= "neural system" WHEN physiological_context
 "CNS" ~= "central nervous system"
 "PNS" ~= "peripheral nervous system"
 "action potential" ~= "regenerative electrical membrane signal"
 "EPSP" ~= "excitatory postsynaptic potential"
 "IPSP" ~= "inhibitory postsynaptic potential"
}

CONFIDENCE NervousSystemAssertion {
 INPUTS: [electrophysiological_support, anatomical_support, neurochemical_support, imaging_support, functional_support, perturbation_support, replication, source_independence, contextual_consistency, semantic_consistency]
 SCORE := weighted_sum(INPUTS)
 LEVEL :=
  IF SCORE >= 0.90 THEN "very_high"
  ELSE IF SCORE >= 0.75 THEN "high"
  ELSE IF SCORE >= 0.55 THEN "moderate"
  ELSE IF SCORE >= 0.35 THEN "low"
  ELSE "uncertain"
}

RULE ActionPotentialInference {
 IF rapid_regenerative_membrane_voltage_change
 AND voltage_dependent_ionic_mechanism IS_SUPPORTED
 THEN ActionPotential MAY_BE_INFERRED
}

RULE SynapticTransmissionInference {
 IF presynaptic_activity precedes_transmitter_release
 AND postsynaptic_receptor_response_follows
 THEN ChemicalSynapticTransmission MAY_BE_SUPPORTED
}

RULE CircuitFunctionInference {
 IF targeted_circuit_perturbation reproducibly_changes neural_or_behavioural_output
 THEN circuit_function_relationship MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF neural_activity correlates_with behaviour_or_physiological_state
 THEN DO_NOT_INFER causal_neural_function
 WITHOUT mechanistic_or_interventional_evidence
}

QUERY NervousSystemLookup(context_identifier) {
 RETURN [central_nervous_system, peripheral_nervous_system, neural_regions, neurons, glia, circuits, sensory_systems, motor_systems, autonomic_systems, measurements, evidence, confidence]
}

QUERY NeuronLookup(neuron_identifier) {
 RETURN [cell_type, morphology, membrane_properties, ion_channels, neurotransmitters, receptors, synaptic_inputs, outputs, firing_properties, evidence, confidence]
}

QUERY NeuralCircuitLookup(circuit_identifier) {
 RETURN [component_neurons, synapses, inputs, outputs, neurotransmitters, connectivity, physiological_function, plasticity, perturbation_evidence, confidence]
}

UPDATE_MODEL {
 ON new_nervous_system_evidence:
  validate_provenance()
  identify_organism_and_developmental_context()
  normalize_neural_region_and_cell_identifiers()
  normalize_neurotransmitter_receptor_and_channel_identifiers()
  capture_physiological_state_and_stimulus()
  capture_measurement_method_and_timepoint()
  map_neural_connectivity()
  map_electrophysiological_and_synaptic_properties()
  map_sensory_motor_and_autonomic_relationships()
  compare_existing_neural_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_nervous_system_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [nervous_system_region, neuron_identity, membrane_potential, action_potential, synaptic_signalling, sensory_motor_context, autonomic_context, physiological_state, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_species_context, preserve_neural_region, preserve_cell_type, preserve_physiological_state, distinguish_CNS_from_PNS, distinguish_chemical_from_electrical_synapse, distinguish_EPSP_from_IPSP, distinguish_neural_activity_from_causal_function, distinguish_synaptic_plasticity_from_learning_itself, preserve_uncertainty]
}

VALIDATE {
 REQUIRE NervousSystem
 REQUIRE CentralNervousSystem
 REQUIRE PeripheralNervousSystem
 REQUIRE Neuron
 REQUIRE GlialCell
 REQUIRE MembranePotential
 REQUIRE ActionPotential
 REQUIRE Synapse
 REQUIRE Neurotransmission
 REQUIRE SensoryTransduction
 REQUIRE MotorControl
 REQUIRE AutonomicNervousSystem
 REQUIRE NeuralCircuit
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT CentralNervousSystem != PeripheralNervousSystem
 ASSERT ChemicalSynapse != ElectricalSynapse
 ASSERT EPSP != IPSP
 ASSERT neural_activity != causal_function
 ASSERT synaptic_plasticity != proof_of_learning
}

FLOW_HASH {
 ALGORITHM: SHA-256
 INPUT: canonicalize(entities, relations, processes, rules, semantic_equivalence, confidence_model, update_model, ai_consumption)
 PURPOSE: integrity_and_version_tracking
}

END flow "NervousSystemOntology"