@prefix tvbo: .
@prefix skos: .
@prefix rdfs: .
@prefix owl: .
@prefix obo: .
@prefix dc: .
@prefix dcterms: .
@prefix xsd: .
@prefix UBERON: .
@prefix CL: .
@prefix GO: .
@prefix MESH: .
#
# ─────────────────────────────────────────────────────────────────
# Ontology header.
# ─────────────────────────────────────────────────────────────────
#
a owl:Ontology ;
dcterms:title "TVB-O hand-authored axioms layer"@en ;
dcterms:description "Axioms layered on top of `tvb-o-struct.owl` (LinkML-generated). Captures statements LinkML cannot express: SKOS anchoring of abstract concepts, backend/task/capability vocabulary, biological-substrate links, and dynamical-systems annotations."@en ;
dcterms:license ;
dcterms:creator "TVB-O contributors" ;
rdfs:seeAlso .
# Property declarations needed for OWL DL cleanliness.
dcterms:subject a owl:AnnotationProperty .
dcterms:license a owl:AnnotationProperty .
dcterms:creator a owl:AnnotationProperty .
dcterms:title a owl:AnnotationProperty .
dcterms:description a owl:AnnotationProperty .
#
# ─────────────────────────────────────────────────────────────────
# §4.0 SKOS anchoring of abstract concepts.
# ─────────────────────────────────────────────────────────────────
#
# Seven abstract concepts that have no concrete YAML parameter to
# attach a `grounding:` slot to. Anchored to upstream GO biological-
# process terms via `skos:broadMatch` only when the GO term genuinely
# subsumes the concept; otherwise no mapping is asserted.
#
tvbo:CouplingInput a skos:Concept ;
skos:prefLabel "CouplingInput"@en ;
rdfs:comment "Aggregate input arriving at a node from connected nodes; modelled as the postsynaptic potential induced by long-range projections."@en ;
rdfs:seeAlso tvbo:PostsynapticPotential .
tvbo:Excitation a skos:Concept ;
rdfs:label "Excitation"@en ;
skos:prefLabel "Excitation"@en ;
rdfs:comment "Generic depolarising synaptic effect; abstract parent of model-specific excitatory currents and conductances."@en ;
skos:broadMatch obo:GO_0060079 . # excitatory postsynaptic potential
tvbo:Inhibition a skos:Concept ;
rdfs:label "Inhibition"@en ;
skos:prefLabel "Inhibition"@en ;
rdfs:comment "Generic hyperpolarising synaptic effect; abstract parent of model-specific inhibitory currents and conductances."@en ;
skos:broadMatch obo:GO_0060080 . # inhibitory postsynaptic potential
tvbo:EIBalance a skos:Concept ;
rdfs:label "E/I balance"@en ;
skos:prefLabel "E/I balance"@en ;
rdfs:comment "Dynamic equilibrium between excitatory and inhibitory drive."@en ;
skos:broadMatch obo:GO_0099177 . # regulation of trans-synaptic signaling
tvbo:FeedbackScaling a skos:Concept ;
rdfs:label "FeedbackScaling"@en ;
skos:prefLabel "FeedbackScaling"@en ;
rdfs:comment "Multiplicative gain applied to recurrent feedback. Control-theoretic concept with no faithful upstream GO mapping."@en .
tvbo:InternalCoupling a skos:Concept ;
rdfs:label "InternalCoupling"@en ;
skos:prefLabel "InternalCoupling"@en ;
rdfs:comment "Within-population synaptic coupling, distinct from long-range inter-node coupling."@en ;
skos:broadMatch obo:GO_0007268 . # chemical synaptic transmission
tvbo:TimeScaling a skos:Concept ;
rdfs:label "TimeScaling"@en ;
skos:prefLabel "TimeScaling"@en ;
rdfs:comment "Time-constant or rate parameter that sets the temporal scale of a dynamical variable. No faithful upstream GO mapping (GO_0050789 was rejected as overly generic)."@en .
#
# ─────────────────────────────────────────────────────────────────
# §4.1 Technical axioms — backends, simulation tasks, capabilities.
# ─────────────────────────────────────────────────────────────────
#
# Class hierarchy:
# Backend (a backend / simulation engine)
# SimulationTask (a computational job a user requests)
# BackendCapability (a feature a backend either provides or lacks)
#
# Object properties:
# tvbo:supportsTask Backend -> SimulationTask
# tvbo:providesCapability Backend -> BackendCapability
# tvbo:executableOn Dynamics | SimulationExperiment -> Backend
#
tvbo:Backend a owl:Class ;
rdfs:label "Backend"@en ;
rdfs:comment "A code-generation or simulation backend (JAX, TVB, PyRates, tvboptim, NetworkDynamics.jl, BifurcationKit.jl)."@en .
tvbo:SimulationTask a owl:Class ;
rdfs:label "Simulation task"@en ;
rdfs:comment "A computational task: forward integration in some formalism, parameter exploration, gradient-based optimisation, numerical continuation, or bifurcation analysis."@en .
tvbo:BackendCapability a owl:Class ;
rdfs:label "Backend capability"@en ;
rdfs:comment "A feature a backend either provides or lacks (autodiff, JIT, GPU, vectorised RNG, delay buffer, stochastic solver, stiff solver, continuation solver, code generation, etc.). Used to gate task support."@en .
tvbo:supportsTask a owl:ObjectProperty ;
rdfs:domain tvbo:Backend ;
rdfs:range tvbo:SimulationTask ;
rdfs:label "supports task"@en .
tvbo:providesCapability a owl:ObjectProperty ;
rdfs:domain tvbo:Backend ;
rdfs:range tvbo:BackendCapability ;
rdfs:label "provides capability"@en .
tvbo:executableOn a owl:ObjectProperty ;
rdfs:range tvbo:Backend ;
rdfs:label "executable on"@en .
# Simulation tasks (instances) — organised by mathematical formalism.
tvbo:ODEIntegration a tvbo:SimulationTask ; rdfs:label "ODE integration"@en ;
rdfs:comment "Forward integration of a deterministic ordinary differential equation."@en .
tvbo:DDEIntegration a tvbo:SimulationTask ; rdfs:label "DDE integration"@en ;
rdfs:comment "Forward integration of a delay differential equation (e.g. long-range axonal delays)."@en .
tvbo:SDEIntegration a tvbo:SimulationTask ; rdfs:label "SDE integration"@en ;
rdfs:comment "Forward integration of a stochastic differential equation."@en .
tvbo:SDDEIntegration a tvbo:SimulationTask ; rdfs:label "SDDE integration"@en ;
rdfs:comment "Forward integration of a stochastic delay differential equation."@en .
tvbo:RDEIntegration a tvbo:SimulationTask ; rdfs:label "RDE integration"@en ;
rdfs:comment "Forward integration of a random differential equation: parameters drawn from a distribution (Bayesian / ensemble simulation)."@en .
tvbo:EventDrivenIntegration a tvbo:SimulationTask ; rdfs:label "Event-driven integration"@en ;
rdfs:comment "Spike-based or hybrid event-driven simulation of a neural network."@en .
tvbo:NumericalContinuation a tvbo:SimulationTask ; rdfs:label "Numerical continuation"@en ;
rdfs:comment "Tracking of equilibria, periodic orbits, or invariant manifolds as a parameter is varied."@en .
tvbo:BifurcationAnalysis a tvbo:SimulationTask ; rdfs:label "Bifurcation analysis"@en ;
rdfs:comment "Detection and classification of bifurcations along a continuation branch."@en .
tvbo:ParameterExploration a tvbo:SimulationTask ; rdfs:label "Parameter exploration"@en .
tvbo:GradientBasedOptimization a tvbo:SimulationTask ; rdfs:label "Gradient-based optimisation"@en .
# Backend capabilities (instances).
tvbo:Autodiff a tvbo:BackendCapability ; rdfs:label "Automatic differentiation"@en .
tvbo:JITCompilation a tvbo:BackendCapability ; rdfs:label "Just-in-time compilation"@en .
tvbo:GPUSupport a tvbo:BackendCapability ; rdfs:label "GPU execution"@en .
tvbo:VectorizedRNG a tvbo:BackendCapability ; rdfs:label "Vectorised RNG"@en .
tvbo:NumPyExecution a tvbo:BackendCapability ; rdfs:label "NumPy execution"@en .
tvbo:BuiltinModelLibrary a tvbo:BackendCapability ; rdfs:label "Built-in model library"@en .
tvbo:CodeGeneration a tvbo:BackendCapability ; rdfs:label "Symbolic code generation"@en ;
rdfs:comment "Backend emits standalone simulator source code from a model specification."@en .
tvbo:NetworkXTopology a tvbo:BackendCapability ; rdfs:label "NetworkX topology API"@en .
tvbo:JuliaJIT a tvbo:BackendCapability ; rdfs:label "Julia JIT"@en .
tvbo:DiffEqIntegrators a tvbo:BackendCapability ; rdfs:label "DifferentialEquations.jl integrators"@en .
tvbo:ContinuationSolver a tvbo:BackendCapability ; rdfs:label "Continuation solver"@en .
tvbo:DelayHistoryBuffer a tvbo:BackendCapability ; rdfs:label "Delay history buffer"@en ;
rdfs:comment "Storage and interpolation of past states required for DDE/SDDE integration."@en .
tvbo:StochasticSolver a tvbo:BackendCapability ; rdfs:label "Stochastic solver"@en .
tvbo:StiffSolver a tvbo:BackendCapability ; rdfs:label "Stiff solver"@en .
# Backends (instances) and their task / capability declarations.
tvbo:JAX a tvbo:Backend ;
rdfs:label "JAX"@en ;
tvbo:supportsTask tvbo:ODEIntegration, tvbo:SDEIntegration,
tvbo:ParameterExploration, tvbo:GradientBasedOptimization ;
tvbo:providesCapability tvbo:Autodiff, tvbo:JITCompilation, tvbo:GPUSupport,
tvbo:VectorizedRNG, tvbo:CodeGeneration .
tvbo:TVB a tvbo:Backend ;
rdfs:label "TVB"@en ;
tvbo:supportsTask tvbo:ODEIntegration, tvbo:DDEIntegration,
tvbo:SDEIntegration, tvbo:SDDEIntegration,
tvbo:ParameterExploration ;
tvbo:providesCapability tvbo:NumPyExecution, tvbo:BuiltinModelLibrary,
tvbo:DelayHistoryBuffer, tvbo:StochasticSolver .
tvbo:PyRates a tvbo:Backend ;
rdfs:label "PyRates"@en ;
tvbo:supportsTask tvbo:ODEIntegration, tvbo:DDEIntegration ;
tvbo:providesCapability tvbo:CodeGeneration, tvbo:NetworkXTopology,
tvbo:DelayHistoryBuffer .
tvbo:tvboptim a tvbo:Backend ;
rdfs:label "tvboptim"@en ;
tvbo:supportsTask tvbo:ODEIntegration, tvbo:SDEIntegration,
tvbo:GradientBasedOptimization ;
tvbo:providesCapability tvbo:Autodiff, tvbo:JITCompilation, tvbo:StochasticSolver,
tvbo:CodeGeneration .
tvbo:NetworkDynamics a tvbo:Backend ;
rdfs:label "NetworkDynamics.jl"@en ;
tvbo:supportsTask tvbo:ODEIntegration, tvbo:DDEIntegration,
tvbo:SDEIntegration, tvbo:SDDEIntegration,
tvbo:ParameterExploration ;
tvbo:providesCapability tvbo:JuliaJIT, tvbo:DiffEqIntegrators,
tvbo:DelayHistoryBuffer, tvbo:StochasticSolver, tvbo:StiffSolver .
tvbo:BifurcationKit a tvbo:Backend ;
rdfs:label "BifurcationKit.jl"@en ;
tvbo:supportsTask tvbo:NumericalContinuation, tvbo:BifurcationAnalysis ;
tvbo:providesCapability tvbo:ContinuationSolver, tvbo:JuliaJIT .
#
# ─────────────────────────────────────────────────────────────────
# §4.2 Biological substrate axioms.
# ─────────────────────────────────────────────────────────────────
#
tvbo:modelsAnatomicalRegion a owl:ObjectProperty ;
rdfs:label "models anatomical region"@en ;
rdfs:comment "Anatomical region(s) the Dynamics model is intended to represent. Range: UBERON terms."@en .
tvbo:modelsCellType a owl:ObjectProperty ;
rdfs:label "models cell type"@en ;
rdfs:comment "Cell type(s) whose collective dynamics the model represents. Range: CL terms."@en .
tvbo:modelsNeurotransmitterSystem a owl:ObjectProperty ;
rdfs:label "models neurotransmitter system"@en ;
rdfs:comment "Neurotransmitter system(s) whose synaptic dynamics the model represents. Range: GO biological-process terms."@en .
#
# ─────────────────────────────────────────────────────────────────
# §4.3 Dynamical-systems axioms.
# ─────────────────────────────────────────────────────────────────
#
# All `DynamicalProperty` siblings and their named members (Excitable,
# Hopf, FixedPoint, ...) are owl:Class entities so subtyping works
# (e.g. SubcriticalHopf ⊑ Hopf) without OWL Full punning. Per-model
# bifurcation events are reified through `tvbo:BifurcationEvent`.
#
tvbo:DynamicalProperty a owl:Class ;
rdfs:label "Dynamical property"@en ;
rdfs:comment "Top-level grouping for qualitative phase-space properties."@en .
tvbo:DynamicalRegime a owl:Class ; rdfs:subClassOf tvbo:DynamicalProperty ;
rdfs:label "Dynamical regime"@en .
tvbo:Bifurcation a owl:Class ; rdfs:subClassOf tvbo:DynamicalProperty ;
rdfs:label "Bifurcation"@en .
tvbo:Attractor a owl:Class ; rdfs:subClassOf tvbo:DynamicalProperty ;
rdfs:label "Attractor"@en .
tvbo:Stochasticity a owl:Class ; rdfs:subClassOf tvbo:DynamicalProperty ;
rdfs:label "Stochasticity character"@en ;
rdfs:comment "Stochasticity character of the model definition itself, independent of any optional integrator-level noise injection."@en .
# Regime classes.
tvbo:Excitable a owl:Class ; rdfs:subClassOf tvbo:DynamicalRegime ; rdfs:label "Excitable"@en .
tvbo:Oscillatory a owl:Class ; rdfs:subClassOf tvbo:DynamicalRegime ; rdfs:label "Oscillatory"@en .
tvbo:Bistable a owl:Class ; rdfs:subClassOf tvbo:DynamicalRegime ; rdfs:label "Bistable"@en .
tvbo:Multistable a owl:Class ; rdfs:subClassOf tvbo:DynamicalRegime ; rdfs:label "Multistable"@en .
tvbo:Chaotic a owl:Class ; rdfs:subClassOf tvbo:DynamicalRegime ; rdfs:label "Chaotic"@en .
tvbo:Quiescent a owl:Class ; rdfs:subClassOf tvbo:DynamicalRegime ; rdfs:label "Quiescent"@en .
tvbo:Bursting a owl:Class ; rdfs:subClassOf tvbo:DynamicalRegime ; rdfs:label "Bursting"@en .
# Bifurcation classes.
tvbo:SaddleNode a owl:Class ; rdfs:subClassOf tvbo:Bifurcation ; rdfs:label "Saddle-node"@en .
tvbo:Hopf a owl:Class ; rdfs:subClassOf tvbo:Bifurcation ; rdfs:label "Hopf"@en .
tvbo:SubcriticalHopf a owl:Class ; rdfs:subClassOf tvbo:Hopf ; rdfs:label "Subcritical Hopf"@en .
tvbo:SupercriticalHopf a owl:Class ; rdfs:subClassOf tvbo:Hopf ; rdfs:label "Supercritical Hopf"@en .
tvbo:Pitchfork a owl:Class ; rdfs:subClassOf tvbo:Bifurcation ; rdfs:label "Pitchfork"@en .
tvbo:Transcritical a owl:Class ; rdfs:subClassOf tvbo:Bifurcation ; rdfs:label "Transcritical"@en .
tvbo:HomoclinicBifurcation a owl:Class ; rdfs:subClassOf tvbo:Bifurcation ; rdfs:label "Homoclinic"@en .
tvbo:FoldOfLimitCycles a owl:Class ; rdfs:subClassOf tvbo:Bifurcation ; rdfs:label "Fold of limit cycles"@en .
tvbo:PeriodDoubling a owl:Class ; rdfs:subClassOf tvbo:Bifurcation ; rdfs:label "Period doubling"@en .
tvbo:BogdanovTakens a owl:Class ; rdfs:subClassOf tvbo:Bifurcation ; rdfs:label "Bogdanov-Takens"@en .
# Attractor classes.
tvbo:FixedPoint a owl:Class ; rdfs:subClassOf tvbo:Attractor ; rdfs:label "Fixed point"@en .
tvbo:LimitCycle a owl:Class ; rdfs:subClassOf tvbo:Attractor ; rdfs:label "Limit cycle"@en .
tvbo:Torus a owl:Class ; rdfs:subClassOf tvbo:Attractor ; rdfs:label "Torus"@en .
tvbo:StrangeAttractor a owl:Class ; rdfs:subClassOf tvbo:Attractor ; rdfs:label "Strange attractor"@en .
# Stochasticity classes.
tvbo:Deterministic a owl:Class ; rdfs:subClassOf tvbo:Stochasticity ; rdfs:label "Deterministic"@en .
tvbo:AdditiveNoise a owl:Class ; rdfs:subClassOf tvbo:Stochasticity ; rdfs:label "Additive noise"@en .
tvbo:MultiplicativeNoise a owl:Class ; rdfs:subClassOf tvbo:Stochasticity ; rdfs:label "Multiplicative noise"@en .
tvbo:ColoredNoise a owl:Class ; rdfs:subClassOf tvbo:Stochasticity ; rdfs:label "Coloured noise"@en .
# Object / data properties on Dynamics models.
tvbo:exhibitsRegime a owl:ObjectProperty ;
rdfs:label "exhibits regime"@en ;
rdfs:comment "Object is a Regime class (open-world: model may admit additional regimes for parameter values not yet catalogued)."@en .
tvbo:exhibitsBifurcation a owl:ObjectProperty ;
rdfs:range tvbo:BifurcationEvent ;
rdfs:label "exhibits bifurcation"@en ;
rdfs:comment "Range is a reified BifurcationEvent that records the bifurcation type, the locus parameter, and (optionally) the critical value."@en .
tvbo:hasAttractor a owl:ObjectProperty ;
rdfs:label "has attractor"@en .
tvbo:hasStochasticityCharacter a owl:ObjectProperty, owl:FunctionalProperty ;
rdfs:label "has stochasticity character"@en ;
rdfs:comment "Intrinsic stochasticity of the model definition itself. A model whose equations are deterministic but is integrated with additive noise via the Integrator is still tvbo:Deterministic here."@en .
tvbo:phaseSpaceDimension a owl:DatatypeProperty, owl:FunctionalProperty ;
rdfs:range xsd:positiveInteger ;
rdfs:label "phase-space dimension"@en .
tvbo:hasTimescaleSeparation a owl:DatatypeProperty ;
rdfs:range xsd:boolean ;
rdfs:label "has timescale separation"@en .
tvbo:hasConservedQuantity a owl:DatatypeProperty ;
rdfs:range xsd:boolean ;
rdfs:label "has conserved quantity"@en .
#
# Reified bifurcation event.
#
# A bifurcation event ties (i) the bifurcation type, (ii) the parameter
# along which the bifurcation occurs, and (iii) the model that exhibits
# it. The parameter range is left open because parameter IRIs are minted
# inside the per-model namespaces by the schema-generated struct OWL.
#
tvbo:BifurcationEvent a owl:Class ;
rdfs:label "Bifurcation event"@en ;
rdfs:comment "Reified record of a bifurcation in a specific model along a specific parameter."@en .
tvbo:bifurcationType a owl:ObjectProperty ;
rdfs:domain tvbo:BifurcationEvent ;
rdfs:label "bifurcation type"@en ;
rdfs:comment "Object is a Bifurcation class (e.g. tvbo:Hopf). Encoded as a class so DL reasoners can use the subClassOf hierarchy on the Bifurcation tree."@en .
tvbo:bifurcationParameter a owl:ObjectProperty ;
rdfs:domain tvbo:BifurcationEvent ;
rdfs:label "bifurcation parameter"@en ;
rdfs:comment "Parameter (CURIE into the per-model parameter namespace) along which the bifurcation is observed."@en .
tvbo:criticalValue a owl:DatatypeProperty, owl:FunctionalProperty ;
rdfs:domain tvbo:BifurcationEvent ;
rdfs:range xsd:double ;
rdfs:label "critical value"@en .
#
# ─────────────────────────────────────────────────────────────────
# §4.4 Model features (intrinsic structural traits, distinct from
# backend capabilities).
# ─────────────────────────────────────────────────────────────────
#
tvbo:ModelFeature a owl:Class ;
rdfs:label "Model feature"@en ;
rdfs:comment "Intrinsic structural trait of a Dynamics model (e.g. sigmoid activation, fast-slow decomposition, E/I subpopulations). Distinct from BackendCapability: a feature is what the model has, a capability is what a backend provides."@en .
tvbo:hasModelFeature a owl:ObjectProperty ;
rdfs:range tvbo:ModelFeature ;
rdfs:label "has model feature"@en .
tvbo:SigmoidActivation a tvbo:ModelFeature ; rdfs:label "Sigmoid activation"@en .
tvbo:FastSlowDecomposition a tvbo:ModelFeature ; rdfs:label "Fast-slow decomposition"@en .
tvbo:ExcitatoryInhibitorySubpopulations
a tvbo:ModelFeature ; rdfs:label "Excitatory/inhibitory subpopulations"@en .
#
# ─────────────────────────────────────────────────────────────────
# Per-model briefs (pilot: JansenRit, Epileptor, ReducedWongWang).
# ─────────────────────────────────────────────────────────────────
#
tvbo:JansenRit
skos:prefLabel "Jansen-Rit"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ; # cerebral cortex
tvbo:modelsCellType CL:0000598, CL:0000099 ; # pyramidal, interneuron
tvbo:modelsNeurotransmitterSystem
GO:0035249, # glutamatergic synaptic transmission
GO:0007214 ; # GABAergic synaptic transmission
tvbo:phaseSpaceDimension 6 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Quiescent ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation false ;
tvbo:hasModelFeature tvbo:SigmoidActivation .
tvbo:Epileptor
rdfs:label "Epileptor"@en ;
tvbo:modelsAnatomicalRegion UBERON:0002728 ; # hippocampus (mesial temporal lobe)
dcterms:subject MESH:D004827 ; # Epilepsy
tvbo:phaseSpaceDimension 6 ;
tvbo:exhibitsRegime tvbo:Bursting, tvbo:Bistable, tvbo:Oscillatory ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:SaddleNode ] ,
[ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:HomoclinicBifurcation ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasTimescaleSeparation true ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasModelFeature tvbo:FastSlowDecomposition .
tvbo:ReducedWongWang
skos:prefLabel "Reduced Wong-Wang"@en ;
tvbo:modelsCellType CL:0000598, CL:0000099 ; # pyramidal, interneuron
tvbo:modelsNeurotransmitterSystem GO:0035249, # glutamatergic
GO:0007214 ; # GABAergic
tvbo:phaseSpaceDimension 1 ;
tvbo:exhibitsRegime tvbo:Bistable, tvbo:Multistable ;
tvbo:hasAttractor tvbo:FixedPoint ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation false ;
tvbo:hasModelFeature tvbo:ExcitatoryInhibitorySubpopulations .
#
# ─────────────────────────────────────────────────────────────────
# Per-model briefs (full coverage of canonical mean-field models).
# ─────────────────────────────────────────────────────────────────
#
# Each brief asserts only properties that are supported by the
# original publication and the YAML definition. Open-world semantics
# apply: absence of an axiom does not imply its negation.
#
# Reduced Wong-Wang variants — share E/I architecture and cortical scope.
tvbo:ReducedWongWangExcInh
skos:prefLabel "Reduced Wong-Wang (E/I)"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:modelsCellType CL:0000598, CL:0000099 ;
tvbo:modelsNeurotransmitterSystem GO:0035249, GO:0007214 ;
tvbo:phaseSpaceDimension 2 ;
tvbo:exhibitsRegime tvbo:Bistable, tvbo:Multistable ;
tvbo:hasAttractor tvbo:FixedPoint ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation false ;
tvbo:hasModelFeature tvbo:ExcitatoryInhibitorySubpopulations .
tvbo:ReducedWongWangFunc
rdfs:label "Reduced Wong-Wang (functional)"@en ;
skos:prefLabel "Reduced Wong-Wang (functional)"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:phaseSpaceDimension 1 ;
tvbo:exhibitsRegime tvbo:Bistable ;
tvbo:hasAttractor tvbo:FixedPoint ;
tvbo:hasStochasticityCharacter tvbo:Deterministic .
tvbo:ReducedWongWangTvboptim
skos:prefLabel "Reduced Wong-Wang (tvboptim)"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:phaseSpaceDimension 1 ;
tvbo:exhibitsRegime tvbo:Bistable ;
tvbo:hasAttractor tvbo:FixedPoint ;
tvbo:hasStochasticityCharacter tvbo:Deterministic .
# Jansen-Rit family — 6-D cortical column with sigmoid activation.
tvbo:Jansen1995
rdfs:label "Jansen 1995"@en ;
skos:prefLabel "Jansen 1995"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:modelsCellType CL:0000598, CL:0000099 ;
tvbo:modelsNeurotransmitterSystem GO:0035249, GO:0007214 ;
tvbo:phaseSpaceDimension 6 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Quiescent ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation false ;
tvbo:hasModelFeature tvbo:SigmoidActivation .
tvbo:JansenRit1995
skos:prefLabel "Jansen-Rit 1995"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:phaseSpaceDimension 6 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Quiescent ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasModelFeature tvbo:SigmoidActivation .
tvbo:ZetterbergJansen
skos:prefLabel "Zetterberg-Jansen"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:phaseSpaceDimension 6 ;
tvbo:exhibitsRegime tvbo:Oscillatory ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasModelFeature tvbo:SigmoidActivation .
# Wilson-Cowan — 2-D E/I cortical mean field.
tvbo:WilsonCowan
skos:prefLabel "Wilson-Cowan"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:modelsCellType CL:0000598, CL:0000099 ;
tvbo:modelsNeurotransmitterSystem GO:0035249, GO:0007214 ;
tvbo:phaseSpaceDimension 2 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Bistable, tvbo:Quiescent ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ,
[ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:SaddleNode ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation false ;
tvbo:hasModelFeature tvbo:SigmoidActivation,
tvbo:ExcitatoryInhibitorySubpopulations .
# Generic 2-D oscillator (FitzHugh-Nagumo-like normal form).
tvbo:Generic2dOscillator
skos:prefLabel "Generic 2-D oscillator"@en ;
tvbo:phaseSpaceDimension 2 ;
tvbo:exhibitsRegime tvbo:Excitable, tvbo:Oscillatory, tvbo:Bistable ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ,
[ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:SaddleNode ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation true .
# Generic linear — used as null/baseline reference.
tvbo:GenericLinear
skos:prefLabel "Generic linear"@en ;
tvbo:phaseSpaceDimension 1 ;
tvbo:exhibitsRegime tvbo:Quiescent ;
tvbo:hasAttractor tvbo:FixedPoint ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation false .
# Supercritical Hopf normal form.
tvbo:SupHopf
skos:prefLabel "Supercritical Hopf"@en ;
tvbo:phaseSpaceDimension 2 ;
tvbo:exhibitsRegime tvbo:Quiescent, tvbo:Oscillatory ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:SupercriticalHopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic .
# Hopfield-style continuous attractor network.
tvbo:Hopfield
skos:prefLabel "Hopfield"@en ;
tvbo:phaseSpaceDimension 2 ;
tvbo:exhibitsRegime tvbo:Multistable ;
tvbo:hasAttractor tvbo:FixedPoint ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasModelFeature tvbo:SigmoidActivation .
# Kuramoto phase oscillator (per-node, 1 SV).
tvbo:Kuramoto
skos:prefLabel "Kuramoto"@en ;
tvbo:phaseSpaceDimension 1 ;
tvbo:exhibitsRegime tvbo:Oscillatory ;
tvbo:hasAttractor tvbo:LimitCycle, tvbo:Torus ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation false .
tvbo:Kuramoto2
rdfs:label "Kuramoto (extended)"@en ;
skos:prefLabel "Kuramoto (extended)"@en ;
tvbo:phaseSpaceDimension 2 ;
tvbo:exhibitsRegime tvbo:Oscillatory ;
tvbo:hasAttractor tvbo:LimitCycle, tvbo:Torus ;
tvbo:hasStochasticityCharacter tvbo:Deterministic .
# Larter-Breakspear — 3-D conductance-based cortical mean field.
tvbo:LarterBreakspear
skos:prefLabel "Larter-Breakspear"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:modelsCellType CL:0000598, CL:0000099 ;
tvbo:modelsNeurotransmitterSystem GO:0035249, GO:0007214 ;
tvbo:phaseSpaceDimension 3 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Bistable, tvbo:Chaotic ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle, tvbo:StrangeAttractor ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation true ;
tvbo:hasModelFeature tvbo:ExcitatoryInhibitorySubpopulations .
# Montbrio-Pazo-Roxin — exact mean field of QIF neurons.
tvbo:MontbrioPazoRoxin
skos:prefLabel "Montbrio-Pazo-Roxin"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:phaseSpaceDimension 2 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Bistable, tvbo:Quiescent ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ,
[ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:SaddleNode ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic .
# Coombes-Byrne — next-generation neural mass (theta-neuron mean field).
tvbo:CoombesByrne
skos:prefLabel "Coombes-Byrne"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:phaseSpaceDimension 4 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Quiescent ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic .
tvbo:CoombesByrne2D
skos:prefLabel "Coombes-Byrne 2D"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:phaseSpaceDimension 2 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Quiescent ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic .
# Dumont-Gutkin — theta-neuron mean field with synaptic dynamics.
tvbo:DumontGutkin
skos:prefLabel "Dumont-Gutkin"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:phaseSpaceDimension 8 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Bistable ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasModelFeature tvbo:ExcitatoryInhibitorySubpopulations .
# Stefanescu-Jirsa reduced HH-like models.
tvbo:StefanescuJirsa2D
skos:prefLabel "Stefanescu-Jirsa 2D"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:phaseSpaceDimension 4 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Bistable, tvbo:Bursting ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation true .
tvbo:StefanescuJirsa3D
skos:prefLabel "Stefanescu-Jirsa 3D"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:phaseSpaceDimension 6 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Bursting, tvbo:Chaotic ;
tvbo:hasAttractor tvbo:LimitCycle, tvbo:StrangeAttractor ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation true .
# Cakan-Obermayer ALN (adaptive linear-nonlinear) cortical mean field.
tvbo:CakanObermayer
skos:prefLabel "Cakan-Obermayer ALN"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:modelsCellType CL:0000598, CL:0000099 ;
tvbo:modelsNeurotransmitterSystem GO:0035249, GO:0007214 ;
tvbo:phaseSpaceDimension 6 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Bistable, tvbo:Quiescent ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation true ;
tvbo:hasModelFeature tvbo:ExcitatoryInhibitorySubpopulations .
# Zerlaut adaptive exponential mean field, first-order.
tvbo:ZerlautAdaptationFirstOrder
skos:prefLabel "Zerlaut (first-order adaptation)"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:modelsCellType CL:0000598, CL:0000099 ;
tvbo:modelsNeurotransmitterSystem GO:0035249, GO:0007214 ;
tvbo:phaseSpaceDimension 5 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Quiescent ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation true ;
tvbo:hasModelFeature tvbo:ExcitatoryInhibitorySubpopulations .
# Tsodyks-Markram short-term plasticity.
tvbo:TsodyksMarkram
skos:prefLabel "Tsodyks-Markram"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:modelsNeurotransmitterSystem GO:0035249 ;
tvbo:phaseSpaceDimension 3 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Quiescent ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic .
# Epileptor variants — all model epileptic seizure dynamics.
tvbo:Epileptor2D
skos:prefLabel "Epileptor 2D"@en ;
tvbo:modelsAnatomicalRegion UBERON:0002728 ;
dcterms:subject MESH:D004827 ;
tvbo:phaseSpaceDimension 2 ;
tvbo:exhibitsRegime tvbo:Bistable, tvbo:Oscillatory ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:SaddleNode ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic .
tvbo:Epileptor3DStefanescuMcDonald
skos:prefLabel "Epileptor 3D (Stefanescu-McDonald)"@en ;
tvbo:modelsAnatomicalRegion UBERON:0002728 ;
dcterms:subject MESH:D004827 ;
tvbo:phaseSpaceDimension 3 ;
tvbo:exhibitsRegime tvbo:Bursting, tvbo:Bistable ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation true ;
tvbo:hasModelFeature tvbo:FastSlowDecomposition .
tvbo:Epileptor5D
skos:prefLabel "Epileptor 5D"@en ;
tvbo:modelsAnatomicalRegion UBERON:0002728 ;
dcterms:subject MESH:D004827 ;
tvbo:phaseSpaceDimension 5 ;
tvbo:exhibitsRegime tvbo:Bursting, tvbo:Bistable, tvbo:Oscillatory ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:SaddleNode ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation true ;
tvbo:hasModelFeature tvbo:FastSlowDecomposition .
tvbo:EpileptorRestingState
skos:prefLabel "Epileptor (resting-state)"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956, UBERON:0002728 ;
dcterms:subject MESH:D004827 ;
tvbo:phaseSpaceDimension 8 ;
tvbo:exhibitsRegime tvbo:Bursting, tvbo:Bistable, tvbo:Oscillatory ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:SaddleNode ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation true ;
tvbo:hasModelFeature tvbo:FastSlowDecomposition .
# Gast-Schmidt-Knosche (synaptic depression / facilitation) variants.
tvbo:GastSchmidtKnosche_SD
skos:prefLabel "Gast-Schmidt-Knosche (synaptic depression)"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:modelsNeurotransmitterSystem GO:0035249 ;
tvbo:phaseSpaceDimension 4 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Quiescent ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic .
tvbo:GastSchmidtKnosche_SF
skos:prefLabel "Gast-Schmidt-Knosche (synaptic facilitation)"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956 ;
tvbo:modelsNeurotransmitterSystem GO:0035249 ;
tvbo:phaseSpaceDimension 4 ;
tvbo:exhibitsRegime tvbo:Oscillatory, tvbo:Quiescent ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:Hopf ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic .
# K-ion exchange model (extracellular potassium dynamics, seizure-like).
tvbo:KIonEx
skos:prefLabel "K-ion exchange"@en ;
tvbo:modelsAnatomicalRegion UBERON:0000956, UBERON:0002728 ;
dcterms:subject MESH:D004827 ;
tvbo:phaseSpaceDimension 5 ;
tvbo:exhibitsRegime tvbo:Bursting, tvbo:Bistable, tvbo:Oscillatory ;
tvbo:exhibitsBifurcation [ a tvbo:BifurcationEvent ;
tvbo:bifurcationType tvbo:SaddleNode ] ;
tvbo:hasAttractor tvbo:FixedPoint, tvbo:LimitCycle ;
tvbo:hasStochasticityCharacter tvbo:Deterministic ;
tvbo:hasTimescaleSeparation true ;
tvbo:hasModelFeature tvbo:FastSlowDecomposition .