Nervous System Ontology

FLOW ALGEBRA
NERVOUS SYSTEM ONTOLOGY
Version: 1.1
Source URL: https://kirethresearch.org/booksai-core/entity-graph/physical-entities/human-entities/nervous-system-ontology-2.html
Authors: Mark Higgins — Sky (Recursive AI)
Site: https://kirethresearch.org
Status: Independent scientific synthesis; source page not independently verified.

01. DOMAIN
ontology_id: kireth:human-entities:nervous-system
parent: kireth:human-entities
subject: NervousSystem
scope: anatomy, physiology, neural signalling, regulation and clinical observation

02. CORE DEFINITION
NervousSystem := organised neural tissues and supporting cells that receive, process and transmit signals to coordinate organism function.

03. TYPE SYSTEM
Human: Organism
NervousSystem: OrganSystem
CentralNervousSystem: NervousSystemDivision
PeripheralNervousSystem: NervousSystemDivision
Brain: Organ
SpinalCord: Organ
Nerve: NeuralStructure
Neuron: Cell
GlialCell: Cell
Synapse: FunctionalJunction
Receptor: SensoryStructure
Effector: MuscleOrGland
ActionPotential: ElectrophysiologicalEvent
NeuralCircuit: ConnectedNeuralNetwork

04. PART-WHOLE AXIOMS
part_of(Brain, CentralNervousSystem)
part_of(SpinalCord, CentralNervousSystem)
part_of(CentralNervousSystem, NervousSystem)
part_of(PeripheralNervousSystem, NervousSystem)
NOTE: types above describe classes; individual part_of assertions require actual instances.

05. RELATION SIGNATURES
part_of(Entity, Entity) -> Boolean
innervates(Nerve, Tissue) -> Boolean
transmits(Neuron, Signal) -> Boolean
synapses_with(Neuron, Neuron) -> Boolean
modulates(Neurotransmitter, Receptor) -> Boolean
responds_to(Receptor, Stimulus) -> Boolean
controls(NeuralCircuit, Effector) -> Boolean
observed_by(NeuralEvent, Measurement) -> Boolean

06. CNS
CentralNervousSystem comprises brain and spinal cord, with integrative, motor and sensory roles.

07. PNS
PeripheralNervousSystem includes nerves and ganglia outside the CNS.
Somatic and autonomic are functional classifications with anatomical overlap.

08. AUTONOMIC DIVISIONS
Sympathetic, parasympathetic and enteric networks coordinate involuntary functions.
Their physiological effects depend on target tissue and receptor subtype.

09. NEURON STRUCTURE
Neuron includes soma, dendrites and axon in typical morphology.
Some neurons depart from this simplified morphology.

10. GLIA
Astrocytes, oligodendrocytes, microglia and ependymal cells support CNS function.
Schwann cells and satellite glia provide peripheral support.

11. MEMBRANE POTENTIAL
V_m := V_inside - V_outside, unit volt.
Ion concentration gradients and membrane permeabilities determine resting potential.

12. NERNST EQUATION
E_ion = (R*T/(z*F))*ln([ion]_out/[ion]_in)
Assumptions: ideal dilute activity approximation, equilibrium for that ion, absolute T.

13. GOLDMAN-HODGKIN-KATZ MODEL
Membrane voltage may be approximated by permeability-weighted ionic concentrations.
Requires explicit ion valences and consistent intracellular/extracellular orientation.

14. ACTION POTENTIAL
ActionPotential is a regenerative membrane voltage excursion in excitable cells.
Voltage-gated channels mediate depolarisation and repolarisation.

15. CONDUCTION
Conduction velocity depends on axon diameter, membrane properties and myelination.
Saltatory conduction occurs in myelinated axons via nodes of Ranvier.

16. SYNAPSES
ChemicalSynapse: presynaptic release -> receptor activation -> postsynaptic response.
ElectricalSynapse: gap-junction-mediated direct electrical coupling.

17. NEUROTRANSMITTERS
Examples: glutamate, GABA, acetylcholine, dopamine, serotonin and noradrenaline.
Excitatory/inhibitory effects depend on receptors and cellular context.

18. SENSORY PATHWAYS
Stimulus -> transduction -> afferent signalling -> CNS processing -> perception or reflex.
Conscious perception is not required for all sensory-motor responses.

19. MOTOR PATHWAYS
Motor commands propagate through descending pathways and peripheral motor units.
Neuromuscular junctions transmit signals to skeletal muscle.

20. REFLEX ARC
ReflexArc := receptor -> afferent -> integration -> efferent -> effector.
Some reflexes involve multiple interneurons; not all are monosynaptic.

21. HOMEOSTASIS
Neural and endocrine mechanisms jointly regulate temperature, breathing and circulation.
Feedback is context-dependent and may be nonlinear.

22. NEURAL CIRCUITS
Circuit := (V, E, W, D)
V: neurons or populations; E: directed connections; W: strengths; D: delays.
Anatomical connectivity does not guarantee effective functional coupling.

23. SIMPLE NEURON MODEL
C_m*dV/dt = -I_ion + I_ext
C_m: capacitance; I_ion: ionic current; I_ext: applied current.
Sign convention must be declared for reproducibility.

24. LEAKY INTEGRATE-AND-FIRE
C_m*dV/dt = -(V-E_L)/R_m + I_ext
If V >= V_threshold, emit spike and reset V to V_reset.
This is an idealised model, not a full biophysical description.

25. HODGKIN-HUXLEY
C_m*dV/dt = I_ext - g_Na*m^3*h*(V-E_Na) - g_K*n^4*(V-E_K) - g_L*(V-E_L)
Gating variables m,h,n evolve via voltage-dependent rate equations.

26. NETWORK DYNAMICS
r_i(t+1) = phi(sum_j W_ij*r_j(t) + u_i(t))
Discrete-time rate model; sampling interval and phi must be specified.

27. SYNAPTIC PLASTICITY
Activity-dependent changes may modify synaptic strength.
Hebbian and spike-timing-dependent rules are models, not universal laws.

28. DEVELOPMENT
Neurulation, neurogenesis, migration, axon guidance and synaptogenesis shape circuits.
Development continues through plasticity and maturation after birth.

29. PROTECTION
Meninges, cerebrospinal fluid, skull and vertebral column protect neural structures.
Blood-brain barrier is selective, not absolutely impermeable.

30. OBSERVATION
EEG: aggregate scalp electrical potentials.
EMG: muscle electrical activity.
MRI: structural imaging; fMRI: indirect haemodynamic correlates of activity.
Nerve conduction studies: peripheral conduction characteristics.

31. MEASUREMENT TYPES
Voltage: volt
Time: second
Frequency: hertz
ConductionVelocity: metre/second
Latency: second
Current: ampere

32. INFERENCE RULES
IF x is a Brain THEN x is an Organ.
IF x is a SpinalCord THEN x is an Organ.
IF x is a Neuron THEN x is a Cell.
IF a signal crosses a ChemicalSynapse THEN neurotransmitter-mediated transmission is possible.
Do not infer a specific neurotransmitter without evidence.

33. SEMANTIC EQUIVALENCE
CNS ~= CentralNervousSystem [exact abbreviation]
PNS ~= PeripheralNervousSystem [exact abbreviation]
nerve != neuron
brain != nervous system
reflex != voluntary movement

34. CONFIDENCE
Established anatomical classifications: high confidence.
Quantitative predictions: conditional on measurement, model and parameters.
Hypothesised connectivity: mark as hypothesis pending evidence.

35. VALIDATION RULES
V01: Every neural anatomical instance has a declared type.
V02: Distinguish cell, tissue, organ and organ system.
V03: Preserve units and sign conventions in electrophysiological equations.
V04: Do not equate structural connectivity with causal influence.
V05: Distinguish observational association from causal mechanism.
V06: Attach provenance and uncertainty to measured values.
V07: Do not infer clinical diagnosis from a single ontology relation.

36. WORKED EXAMPLE: REFLEX
Input: cutaneous stimulus activates sensory receptor.
Transform: afferent impulse -> spinal integration -> motor output.
Output: effector muscle contraction.
Validation: reflex latency depends on pathway length and synaptic delays.

37. WORKED EXAMPLE: CONDUCTION
Given path length L=1.0 m and conduction velocity v=50 m/s.
Propagation time t=L/v=0.020 s.
This excludes synaptic, transduction and neuromuscular delays.

38. KNOWLEDGE GRAPH
Human -> has_system -> NervousSystem
NervousSystem -> has_division -> CentralNervousSystem
NervousSystem -> has_division -> PeripheralNervousSystem
CentralNervousSystem -> includes -> Brain
CentralNervousSystem -> includes -> SpinalCord
Neuron -> communicates_via -> Synapse
SensoryReceptor -> detects -> Stimulus
MotorNeuron -> innervates -> Effector

39. PROVENANCE
source_url: https://kirethresearch.org/booksai-core/entity-graph/physical-entities/human-entities/nervous-system-ontology-2.html
source_verification: not_verified
scientific_basis: standard neuroanatomy and neurophysiology concepts

40. FLOW HASH SPECIFICATION
FLOW_HASH.algorithm: SHA-256
FLOW_HASH.canonicalisation: UTF-8, LF newlines, omit hash-value line
FLOW_HASH.value: compute on canonical final text at ingestion

41. UPDATE MODEL
version: 1.1
update_strategy: versioned semantic diff
review_on: revised anatomical terminology, new experimental evidence, changed models
preserve: stable entity identifiers and provenance history

42. AI CONSUMPTION
mode: typed semantic reasoning
allowed: classification, relation traversal, unit-checked model evaluation
requires: context, provenance, uncertainty, validation
forbidden: unsupported diagnosis, causal inference from correlation alone

43. COMPLETENESS
sections_expected: 43
sections_present: 43
closing_marker_required: true

END FLOW ALGEBRA — NERVOUS SYSTEM ONTOLOGY