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oxford-metadata.ttl
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# Chaste metadata for annotating CellML files representing cardiac electrophysiology models.
# Licence is 3-clause BSD as for Chaste; see end of file for details.
@base <https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata> .
# Allow us to refer to terms in our vocabulary using the concise ':term', rather than <#term> or full URI
@prefix : <https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#> .
# Other vocabularies we use
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
# TODO:
# - Decide on new base URI
# ======================================================================
# Properties to use for annotating datasets
# ======================================================================
:organism
a rdf:Property ;
rdfs:label "identifies the organism this data/model is about" ;
rdfs:range :Species .
:hasTemperature
a rdf:Property ;
rdfs:label "Temperature measurement" .
:cell_type
a rdf:Property ;
rdfs:label "identifies the cell type this data/model is about" ;
rdfs:range :CellType .
:measures
a rdf:Property ;
rdfs:label "Describes which ontology term a CSV column is a measurement of." .
:units
a rdf:Property ;
rdfs:label "The units of a measured quantity" ;
rdfs:comment "The list of allowed values is not kept as an ontology, but is mapped by name to CellML/pint/Sympy definitions." .
:value
rdfs:label "The value of a measured quantity" .
# Maps to OBI measurement_datum
# ======================================================================
# Annotating the species/organism data or models are about
# ======================================================================
:Species
a rdfs:Class ;
rdfs:label "Species" ;
rdfs:comment "The class of typical species found in cardiac models." .
:human
a :Species ;
rdfs:label "Human (Homo Sapiens)" .
:rabbit
a :Species ;
rdfs:label "Rabbit" .
:dog
a :Species ;
rdfs:label "Dog" .
:mammalian
a :Species ;
rdfs:label "Mammalian" ;
rdfs:comment "Unspecified, unknown or mixed mammalian species." .
# etc. TODO
# ======================================================================
# Annotating the cell type data or models are about
# ======================================================================
:CellType
a rdfs:Class ;
rdfs:label "Cell type" ;
rdfs:comment "The class of typical cell types found in cardiac models." .
:hiPSC
a :CellType ;
rdfs:label "Human induced pluripotent stem cell" .
:atrial
a :CellType ;
rdfs:label "Atrial" .
:sino_atrial_node
a :CellType ;
rdfs:label "Sino-atrial node" .
:ventricular
a :CellType ;
rdfs:label "Ventricular" .
:left_ventricular
a :ventricular ;
rdfs:label "Left ventricular" .
:right_ventricular
a :ventricular ;
rdfs:label "Right ventricular" .
:epicardial
a :CellType ;
rdfs:label "(Sub)epicardial" .
:endocardial
a :CellType ;
rdfs:label "(Sub)endocardial" .
# etc. TODO
# ======================================================================
# Classes for model annotation
# ======================================================================
# This class exists purely as a convenient mechanism for our tool in development to assist
# with annotating CellML models, so it can generate a list of potential terms by looking for
# instances of this class. It may disappear in the future (once we integrate other ontologies etc.).
:Annotation
a rdfs:Class ;
rdfs:label "Variable Annotation" ;
rdfs:comment "The class of IRIs that can annotate variables in a CellML model." .
:ImplicitAnnotation
a rdfs:Class ;
rdfs:label "Implicit Variable Annotation" ;
rdfs:comment "The class of IRIs that implicitly annotate variables in a CellML model (i.e. are added automatically by tools)." .
:MultipleUsesAllowed
a rdfs:Class ;
rdfs:label "Annotations that can appear on more than one variable in a model." ;
rdfs:comment "This indicates to the annotation tool that it should allow multiple occurrences." .
:IonicCurrent
a rdfs:Class ;
rdfs:label "Ionic currents" ;
rdfs:comment "All terms that represent a current anywhere in the cell." .
:ConductanceOrPermeability
a rdfs:Class ;
rdfs:label "A maximal conductance or permeability parameter" ;
rdfs:comment "Tags for maximal conductance or permeability when open probability is equal to one (these may be algebraic expressions as well as constants)." .
# The following classes are used to build the tree hierarchy containing the available annotations in the UI.
:Category
a rdfs:Class ;
rdfs:label "A category of annotations" ;
rdfs:comment "A class for classes that contain annotations, used to build a tree hierarchy in the annotation UI." .
:Constant
a :Category ;
rdfs:label "Universal constants" .
:PhysicalProperty
a :Category ;
rdfs:label "Physical properties" .
:CellMembraneCurrentRelated
a :Category ;
rdfs:label "Membrane currents and their properties" ;
rdfs:comment "Annotations associated with currents across the cell membrane." .
:StimulusCurrentRelated
a :CellMembraneCurrentRelated ;
a :ChasteMetadata ;
rdfs:label "Stimulus current and its properties" .
:MembranePumpRelated
a :CellMembraneCurrentRelated ;
rdfs:label "Pumps" ;
rdfs:comment "Terms related to proteins that use energy in ATP to pump ions against their electrochemical gradients." .
:MembraneExchangerRelated
a :CellMembraneCurrentRelated ;
rdfs:label "Exchangers" ;
rdfs:comment "Terms related to proteins that use the energy of one ionic species moving down an electrochemical gradient, to move another species against its gradient." .
:MembraneIonChannelRelated
a :CellMembraneCurrentRelated ;
rdfs:label "Ion channels" ;
rdfs:comment "Terms related to proteins allowing certain ions to flow down their electrochemical gradients." .
:MembranePotassiumChannelRelated
a :MembraneIonChannelRelated ;
rdfs:label "Terms related to potassium ion channels" .
:MembraneSodiumChannelRelated
a :MembraneIonChannelRelated ;
rdfs:label "Terms related to sodium ion channels" .
:MembraneCalciumChannelRelated
a :MembraneIonChannelRelated ;
rdfs:label "Terms related to calcium ion channels" .
:MembraneChlorideChannelRelated
a :MembraneIonChannelRelated ;
rdfs:label "Terms related to chloride ion channels" .
:MembraneMixedChannelRelated
a :MembraneIonChannelRelated ;
rdfs:label "Terms related to mixed ion channels" ;
rdfs:comment "Membrane ion channels that don't fit a more specific categorisation, or transport multiple species." .
:PatchClampProperties
a :Category ;
rdfs:label "Patch clamp properties" ;
rdfs:comment "Properties of the patch clamp experimental setup represented explicitly in models." .
:SRCurrentRelated
a :Category ;
rdfs:label "SR currents" ;
rdfs:comment "Annotations associated with currents across the sarcoplasmic reticulum membrane." .
:SRPumpRelated
a :SRCurrentRelated ;
rdfs:label "Pumps" ;
rdfs:comment "Terms related to proteins in the sarcoplasmic reticulum membrane that use energy in ATP to pump ions against their electrochemical gradients." .
:SRExchangerRelated
a :SRCurrentRelated ;
rdfs:label "Exchangers" .
:SRIonChannelRelated
a :SRCurrentRelated ;
rdfs:label "Ion channels" ;
rdfs:comment "Terms related to proteins in the sarcoplasmic reticulum membrane allowing certain ions to flow down their electrochemical gradients." .
:Concentration
a :Category ;
rdfs:label "Ionic concentrations" .
:CytosolicConcentration
a :Concentration ;
rdfs:label "Cytosolic ionic concentrations" .
:ExtracellularConcentration
a :Concentration ;
rdfs:label "Extracellular ionic concentrations" .
:ExtracellularBathConcentration
a :ExtracellularConcentration ;
rdfs:label "Extracellular ionic concentrations, far from the cell" .
:ExtracellularCleftConcentration
a :ExtracellularConcentration ;
rdfs:label "Extracellular ionic concentrations, close to the cell" .
:SRConcentration
a :Concentration ;
rdfs:label "Ionic concentrations in the SR" .
:CleftConcentration
a :Concentration ;
rdfs:label "Ionic concentrations in the cleft / dyadic space" .
:SubMembraneConcentration
a :Concentration ;
rdfs:label "Ionic concentrations in the sub-membrane space" .
:ChasteMetadata
a :Category ;
rdfs:label "Basic Chaste metadata" ;
rdfs:comment "Core annotations needed for a model to work well with the Chaste simulator." .
:BufferingTerm
a :Category ;
rdfs:label "Buffering" ;
rdfs:comment "Annotations needed for studying and altering ionic buffering." .
:CustomAnnotations
a :Category ;
rdfs:label "Custom annotations" ;
rdfs:comment "Custom annotations in other namespaces referenced by protocols." .
# ======================================================================
# General labels
# ======================================================================
:state_variable
a :ImplicitAnnotation ;
rdfs:label "State variable" ;
rdfs:comment "Indicates a dependent variable in the model. Does not need to be specified explicitly: the Functional Curation tools will automatically annotate all state variables in the modified model." .
:time
a :Annotation ;
a :PhysicalProperty ;
a :ChasteMetadata ;
rdfs:label "Time" ;
rdfs:comment "The independent variable, the simulation time." .
:temperature
a :Annotation ;
a :PhysicalProperty ;
rdfs:label "Temperature" .
:gas_constant
a :Annotation ;
a :Constant ;
rdfs:label "Ideal Gas Constant - R" ;
rdfs:comment "Also known as the Molar or Universal gas constant." .
:faraday_constant
a :Annotation ;
a :Constant ;
rdfs:label "Faraday's constant - F" ;
rdfs:comment "Equal to the electical charge on one mole of electrons." .
:Probability
a :Category ;
rdfs:label "Probability" .
:hodgkin_huxley_gate
a :Annotation ;
a :MultipleUsesAllowed ;
a :Probability ;
a :CellMembraneCurrentRelated ;
rdfs:label "Hodgkin-Huxley Gate" ;
rdfs:comment "For any state variable which is a Hodgkin-Huxley gating variable." .
:markov_model_state
a :Annotation ;
a :MultipleUsesAllowed ;
a :Probability ;
a :CellMembraneCurrentRelated ;
rdfs:label "Markov Model State" ;
rdfs:comment "For any state variable which is a state in a Markov model for an ion channel." .
:not_a_probability_even_though_it_should_be
a :Annotation ;
a :MultipleUsesAllowed ;
a :Probability ;
rdfs:label "Probability that does not stay within 0 ... 1 range" ;
rdfs:comment "This should be a probability but it is not guaranteed to stay within [0,1] because of unusual mathematical formulation. Introduced to prevent checks being generated in code for quantities annotated with this tag" .
# ======================================================================
# Cardiac-Specific Labels
# ======================================================================
# VOLTAGES / POTENTIALS
:membrane_voltage
a :Annotation ;
a :ChasteMetadata ;
a :PhysicalProperty ;
rdfs:label "Voltage across the cell membrane" .
# These are intended to refer to outer cell membrane, new tags should be
# introduced for SR membrane, mitochondrial membranes etc.
:sodium_reversal_potential
a :Annotation ;
a :MembraneSodiumChannelRelated ;
a :Concentration ;
rdfs:label "Sodium reversal potential" ;
rdfs:comment "Reversal potential of sodium ions across the cell membrane" .
:potassium_reversal_potential
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :Concentration ;
rdfs:label "Potassium reversal potential" ;
rdfs:comment "Reversal potential of potassium ions across the cell membrane" .
:rapid_delayed_rectifier_potassium_reversal_potential
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :Concentration ;
rdfs:label "IKr reversal potential" ;
rdfs:comment "Reversal potential for the IKr current across the cell membrane, for when it isn't the general potassium_reversal_potential" .
:slow_delayed_rectifier_potassium_reversal_potential
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :Concentration ;
rdfs:label "IKs reversal potential" ;
rdfs:comment "Reversal potential for the IKs current across the cell membrane, for when it isn't the general potassium_reversal_potential" .
:calcium_reversal_potential
a :Annotation ;
a :MembraneCalciumChannelRelated ;
a :Concentration ;
rdfs:label "Calcium reversal potential" ;
rdfs:comment "Reversal potential of calcium ions across the cell membrane" .
:chloride_reversal_potential
a :Annotation ;
a :MembraneChlorideChannelRelated ;
a :Concentration ;
rdfs:label "Chloride reversal potential" ;
rdfs:comment "Reversal potential of chloride ions across the cell membrane" .
# Membrane properties
:membrane_capacitance
a :Annotation ;
a :PhysicalProperty ;
a :ChasteMetadata ;
rdfs:label "Cell membrane capacitance" .
# =====================================================
# Stimulus Current
# =====================================================
:membrane_stimulus_current
a :Annotation ;
a :StimulusCurrentRelated ;
a :IonicCurrent ;
rdfs:label "Membrane stimulus current" .
:membrane_stimulus_current_duration
a :Annotation ;
a :StimulusCurrentRelated ;
rdfs:label "Membrane stimulus current pulse duration" .
:membrane_stimulus_current_amplitude
a :Annotation ;
a :StimulusCurrentRelated ;
rdfs:label "Membrane stimulus current pulse amplitude" ;
rdfs:comment "This should be negative in order to cause a positive change in voltage." .
:membrane_stimulus_current_period
a :Annotation ;
a :StimulusCurrentRelated ;
rdfs:label "Membrane stimulus current pulse period" .
:membrane_stimulus_current_offset
a :Annotation ;
a :StimulusCurrentRelated ;
rdfs:label "Membrane stimulus current pulse start offset" .
:membrane_stimulus_current_end
a :Annotation ;
a :StimulusCurrentRelated ;
rdfs:label "Membrane stimulus current pulse end time" .
# =====================================================
# Ionic concentrations
# =====================================================
# basic 'intracellular' and 'extracellular'
:extracellular_potassium_concentration
a :Annotation ;
a :ExtracellularConcentration ;
rdfs:label "Extracellular potassium concentration" .
:extracellular_calcium_concentration
a :Annotation ;
a :ExtracellularConcentration ;
rdfs:label "Extracellular calcium concentration" .
:extracellular_sodium_concentration
a :Annotation ;
a :ExtracellularConcentration ;
rdfs:label "Extracellular sodium concentration" .
:extracellular_chloride_concentration
a :Annotation ;
a :ExtracellularConcentration ;
rdfs:label "Extracellular chloride concentration" .
:cytosolic_potassium_concentration
a :Annotation ;
a :CytosolicConcentration ;
rdfs:label "Cytosolic potassium concentration" .
:cytosolic_calcium_concentration
a :Annotation ;
a :CytosolicConcentration ;
rdfs:label "Cytosolic calcium concentration" .
:cytosolic_sodium_concentration
a :Annotation ;
a :CytosolicConcentration ;
rdfs:label "Cytosolic sodium concentration" .
:cytosolic_chloride_concentration
a :Annotation ;
a :CytosolicConcentration ;
rdfs:label "Cytosolic chloride concentration" .
# in Calcium subsystem SR = sarcoplasmic reticulum
:SR_calcium_concentration
a :Annotation ;
a :SRConcentration ;
rdfs:label "Concentration of calcium in the sarcoplasmic reticulum" ;
rdfs:comment "Some models treat the SR as a whole, and do not decompose it into different regions." .
:JSR_calcium_concentration
a :Annotation ;
a :SRConcentration ;
rdfs:label "Concentration of calcium in the junctional sarcoplasmic reticulum" ;
rdfs:comment "The junctional SR is that portion near the RyRs." .
:NSR_calcium_concentration
a :Annotation ;
a :SRConcentration ;
rdfs:label "Concentration of calcium in the network sarcoplasmic reticulum" ;
rdfs:comment "The network SR is the non-junctional part of the SR." .
:dyadic_space_calcium_concentration
a :Annotation ;
a :CleftConcentration ;
rdfs:label "Concentration of calcium in the dyadic sub-space" ;
rdfs:comment "Some models also have a separate dyadic sub-space (cytosol between JSR and t-tubules)." .
:dyadic_space_potassium_concentration
a :Annotation ;
a :CleftConcentration ;
rdfs:label "Concentration of potassium in the dyadic sub-space" ;
rdfs:comment "Some models also have a separate dyadic sub-space (cytosol between JSR and t-tubules)." .
:dyadic_space_sodium_concentration
a :Annotation ;
a :CleftConcentration ;
rdfs:label "Concentration of sodium in the dyadic sub-space" ;
rdfs:comment "Some models also have a separate dyadic sub-space (cytosol between JSR and t-tubules)." .
:dyadic_space_chloride_concentration
a :Annotation ;
a :CleftConcentration ;
rdfs:label "Concentration of chloride ions in the dyadic sub-space" ;
rdfs:comment "Some models also have a separate dyadic sub-space (cytosol between JSR and t-tubules)." .
:submembrane_space_calcium_concentration
a :Annotation ;
a :SubMembraneConcentration ;
rdfs:label "Concentration of calcium ions in the sub-membrane compartment" ;
rdfs:comment "Some models have a separate compartment underlying the entire cell membrane, distinct from the dyadic sub-space." .
:submembrane_space_potassium_concentration
a :Annotation ;
a :SubMembraneConcentration ;
rdfs:label "Concentration of potassium ions in the sub-membrane compartment" ;
rdfs:comment "Some models have a separate compartment underlying the entire cell membrane, distinct from the dyadic sub-space." .
:submembrane_space_sodium_concentration
a :Annotation ;
a :SubMembraneConcentration ;
rdfs:label "Concentration of sodium ions in the sub-membrane compartment" ;
rdfs:comment "Some models have a separate compartment underlying the entire cell membrane, distinct from the dyadic sub-space." .
:submembrane_space_chloride_concentration
a :Annotation ;
a :SubMembraneConcentration ;
rdfs:label "Concentration of chloride ions in the sub-membrane compartment" ;
rdfs:comment "Some models have a separate compartment underlying the entire cell membrane, distinct from the dyadic sub-space." .
# Detailed extra-cellular concentrations
:extracellular_bath_potassium_concentration
a :Annotation ;
a :ExtracellularBathConcentration ;
rdfs:label "Potassium concentration in the extracellular bath" ;
rdfs:comment "Some models divide the extracellular space into 'bath' (far from the cell) and 'cleft' (near the cell)." .
:extracellular_bath_calcium_concentration
a :Annotation ;
a :ExtracellularBathConcentration ;
rdfs:label "Calcium concentration in the extracellular bath" ;
rdfs:comment "Some models divide the extracellular space into 'bath' (far from the cell) and 'cleft' (near the cell)." .
:extracellular_bath_sodium_concentration
a :Annotation ;
a :ExtracellularBathConcentration ;
rdfs:label "Sodium concentration in the extracellular bath" ;
rdfs:comment "Some models divide the extracellular space into 'bath' (far from the cell) and 'cleft' (near the cell)." .
:extracellular_bath_chloride_concentration
a :Annotation ;
a :ExtracellularBathConcentration ;
rdfs:label "Chloride concentration in the extracellular bath" ;
rdfs:comment "Some models divide the extracellular space into 'bath' (far from the cell) and 'cleft' (near the cell)." .
:extracellular_cleft_potassium_concentration
a :Annotation ;
a :ExtracellularCleftConcentration ;
rdfs:label "Potassium concentration in the extracellular cleft" ;
rdfs:comment "Some models divide the extracellular space into 'bath' (far from the cell) and 'cleft' (near the cell)." .
:extracellular_cleft_calcium_concentration
a :Annotation ;
a :ExtracellularCleftConcentration ;
rdfs:label "Calcium concentration in the extracellular cleft" ;
rdfs:comment "Some models divide the extracellular space into 'bath' (far from the cell) and 'cleft' (near the cell)." .
:extracellular_cleft_sodium_concentration
a :Annotation ;
a :ExtracellularCleftConcentration ;
rdfs:label "Sodium concentration in the extracellular cleft" ;
rdfs:comment "Some models divide the extracellular space into 'bath' (far from the cell) and 'cleft' (near the cell)." .
:extracellular_cleft_chloride_concentration
a :Annotation ;
a :ExtracellularCleftConcentration ;
rdfs:label "Chloride concentration in the extracellular cleft" ;
rdfs:comment "Some models divide the extracellular space into 'bath' (far from the cell) and 'cleft' (near the cell)." .
# =====================================================
# BUFFERING TERMS
# =====================================================
:cytosolic_calcium_flux_scaling_from_intrinsic_buffers
a :Annotation ;
a :BufferingTerm ;
rdfs:label "Scaling factor for calcium fluxes in the cytosol due to buffering" ;
rdfs:comment "This term annotates how calcium fluxes in the cytosol are scaled due to intrinsic (natural) buffering" .
:submembrane_space_calcium_flux_scaling_from_intrinsic_buffers
a :Annotation ;
a :BufferingTerm ;
rdfs:label "Scaling factor for calcium fluxes in the submembrane space due to buffering" ;
rdfs:comment "Some models have a separate compartment underlying the entire cell membrane, distinct from the dyadic sub-space. This term annotates how calcium fluxes here are scaled due to buffering" .
:dyadic_space_calcium_flux_scaling_from_intrinsic_buffers
a :Annotation ;
a :BufferingTerm ;
rdfs:label "Scaling factor for calcium fluxes in the dyadic sub-space due to buffering" ;
rdfs:comment "Some models also have a separate dyadic sub-space (cytosol between JSR and t-tubules). This term annotates how calcium fluxes here are scaled due to buffering" .
# =====================================================
# PATCH CLAMP PROPERTIES
# =====================================================
:seal_resistance
a :Annotation ;
a :PatchClampProperties ;
rdfs:label "Patch clamp seal resistance" ;
rdfs:comment "Patch clamp seal resistance" .
:leakage_compensation_percentage
a :Annotation ;
a :PatchClampProperties ;
rdfs:label "Percentage of seal leakage compensation current to include" ;
rdfs:comment "Percentage of seal leakage compensation current to include" .
# =====================================================
# CURRENTS
# =====================================================
# HISTORIC metadata - only for early models lacking components.
:membrane_potassium_current
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :IonicCurrent ;
rdfs:label "Membrane potassium current" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:membrane_potassium_current_conductance
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane potassium current conductance" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:membrane_plateau_potassium_current
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :IonicCurrent ;
rdfs:label "Membrane plateau potassium current" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:membrane_plateau_potassium_current_conductance
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane plateau potassium current conductance" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:potassium_channel_n_gate
a :Annotation ;
a :hodgkin_huxley_gate ;
a :MembranePotassiumChannelRelated ;
rdfs:label "Potassium channel n gate" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:membrane_delayed_rectifier_potassium_current
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :IonicCurrent ;
rdfs:label "Membrane delayed rectifier potassium current" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:membrane_delayed_rectifier_potassium_current_conductance
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane delayed rectifier potassium current conductance" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:rapid_time_dependent_potassium_current_conductance
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Rapid time-dependent potassium current conductance" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:rapid_time_dependent_potassium_current_Xr1_gate
a :Annotation ;
a :hodgkin_huxley_gate ;
a :MembranePotassiumChannelRelated ;
rdfs:label "Rapid time-dependent potassium current Xr1 gate" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:rapid_time_dependent_potassium_current_Xr2_gate
a :Annotation ;
a :hodgkin_huxley_gate ;
a :MembranePotassiumChannelRelated ;
rdfs:label "Rapid time-dependent potassium current Xr2 gate" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:slow_time_dependent_potassium_current_conductance
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Slow time-dependent potassium current conductance" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:slow_time_dependent_potassium_current_Xs_gate
a :Annotation ;
a :hodgkin_huxley_gate ;
a :MembranePotassiumChannelRelated ;
rdfs:label "Slow time-dependent potassium current Xs gate" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:membrane_slow_inward_current
a :Annotation ;
a :MembraneMixedChannelRelated ;
a :IonicCurrent ;
rdfs:label "Membrane slow inward current" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:membrane_slow_inward_current_conductance
a :Annotation ;
a :MembraneMixedChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane slow inward current conductance" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:membrane_leakage_current
a :Annotation ;
a :MembraneMixedChannelRelated ;
a :PatchClampProperties ;
a :IonicCurrent ;
rdfs:label "Membrane leakage current" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
:membrane_leakage_current_conductance
a :Annotation ;
a :MembraneMixedChannelRelated ;
a :PatchClampProperties ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane leakage current conductance" ;
rdfs:comment "Historical metadata - only for early models lacking components." .
# Following entries are MODERN metadata - labels all new models should be able to use.
# ========================================================================
# Sodium currents
# ========================================================================
# I Na (fast)
:membrane_fast_sodium_current
a :Annotation ;
a :MembraneSodiumChannelRelated ;
a :IonicCurrent ;
rdfs:label "Membrane fast sodium current" .
:membrane_fast_sodium_current_conductance
a :Annotation ;
a :MembraneSodiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane fast sodium current conductance" .
:membrane_fast_sodium_current_conductance_scaling_factor
a :Annotation ;
a :MembraneSodiumChannelRelated ;
rdfs:label "Membrane fast sodium current conductance scaling factor" ;
rdfs:comment "A scalar that multiplies the conductance term for this current" .
:membrane_fast_sodium_current_m_gate
a :Annotation ;
a :hodgkin_huxley_gate ;
a :MembraneSodiumChannelRelated ;
rdfs:label "Membrane fast sodium current m gate" .
:membrane_fast_sodium_current_h_gate
a :Annotation ;
a :hodgkin_huxley_gate ;
a :MembraneSodiumChannelRelated ;
rdfs:label "Membrane fast sodium current h gate" .
:membrane_fast_sodium_current_h_gate_tau
a :Annotation ;
a :MembraneSodiumChannelRelated ;
rdfs:label "Membrane fast sodium current h gate tau" .
:membrane_fast_sodium_current_j_gate
a :Annotation ;
a :hodgkin_huxley_gate ;
a :MembraneSodiumChannelRelated ;
rdfs:label "Membrane fast sodium current j gate" .
:membrane_fast_sodium_current_j_gate_tau
a :Annotation ;
a :MembraneSodiumChannelRelated ;
rdfs:label "Membrane fast sodium current j gate tau" .
:membrane_fast_sodium_current_shift_inactivation
a :Annotation ;
a :MembraneSodiumChannelRelated ;
rdfs:label "Membrane fast sodium current shift inactivation" .
:membrane_fast_sodium_current_reduced_inactivation
a :Annotation ;
a :MembraneSodiumChannelRelated ;
rdfs:label "Membrane fast sodium current reduced inactivation" .
# I_Na_L (late or persistent)
:membrane_persistent_sodium_current
a :Annotation ;
a :MembraneSodiumChannelRelated ;
a :IonicCurrent ;
rdfs:label "Membrane persistent sodium current" ;
rdfs:comment "Also known as membrane late sodium current" .
:membrane_persistent_sodium_current_conductance
a :Annotation ;
a :MembraneSodiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane persistent sodium current conductance" ;
rdfs:comment "Also known as membrane late sodium current conductance" .
:membrane_persistent_sodium_current_conductance_scaling_factor
a :Annotation ;
a :MembraneSodiumChannelRelated ;
rdfs:label "Membrane persistent sodium current conductance scaling factor" ;
rdfs:comment "A scalar that multiplies the conductance term for this current" .
# I Na,b (background)
:membrane_background_sodium_current
a :Annotation ;
a :MembraneSodiumChannelRelated ;
a :IonicCurrent ;
rdfs:label "Membrane background sodium current" .
:membrane_background_sodium_current_conductance
a :Annotation ;
a :MembraneSodiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane background sodium current conductance" .
# ========================================================================
# Potassium currents
# ========================================================================
# I Kr
:membrane_rapid_delayed_rectifier_potassium_current
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :IonicCurrent ;
rdfs:label "Membrane rapid delayed rectifier potassium current" .
:membrane_rapid_delayed_rectifier_potassium_current_open_probability
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :Probability ;
rdfs:label "Membrane rapid delayed rectifier potassium current open probability" .
:membrane_rapid_delayed_rectifier_potassium_current_conductance
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane rapid delayed rectifier potassium current conductance" .
:membrane_rapid_delayed_rectifier_potassium_current_conductance_scaling_factor
a :Annotation ;
a :MembranePotassiumChannelRelated ;
rdfs:label "Membrane rapid delayed rectifier potassium current conductance scaling factor" ;
rdfs:comment "A scalar that multiplies the conductance term for this current" .
:membrane_rapid_delayed_rectifier_potassium_current_conductance1
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane rapid delayed rectifier potassium current conductance 1" ;
rdfs:comment "TODO!" .
:membrane_rapid_delayed_rectifier_potassium_current_conductance2
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane rapid delayed rectifier potassium current conductance 2" ;
rdfs:comment "TODO!" .
# I Ks
:membrane_slow_delayed_rectifier_potassium_current
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :IonicCurrent ;
rdfs:label "Membrane slow delayed rectifier potassium current" .
:membrane_slow_delayed_rectifier_potassium_current_conductance
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane slow delayed rectifier potassium current conductance" .
:membrane_slow_delayed_rectifier_potassium_current_conductance_scaling_factor
a :Annotation ;
a :MembranePotassiumChannelRelated ;
rdfs:label "Membrane slow delayed rectifier potassium current conductance scaling factor" ;
rdfs:comment "A scalar that multiplies the conductance term for this current" .
:membrane_slow_delayed_rectifier_potassium_current_xs1_gate_tau
a :Annotation ;
a :MembranePotassiumChannelRelated ;
rdfs:label "Membrane slow delayed rectifier potassium current xs1 gate tau" ;
rdfs:comment "Really a scaling factor for tau" .
:membrane_slow_delayed_rectifier_potassium_current_xs2_gate_tau
a :Annotation ;
a :MembranePotassiumChannelRelated ;
rdfs:label "Membrane slow delayed rectifier potassium current xs2 gate tau" ;
rdfs:comment "Really a scaling factor for tau" .
# I_Kur
:membrane_ultrarapid_delayed_rectifier_potassium_current
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :IonicCurrent ;
rdfs:label "Membrane ultrarapid delayed rectifier potassium current" .
:membrane_ultrarapid_delayed_rectifier_potassium_current_conductance
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane ultrarapid delayed rectifier potassium current conductance" .
:membrane_ultrarapid_delayed_rectifier_potassium_current_conductance_scaling_factor
a :Annotation ;
a :MembranePotassiumChannelRelated ;
rdfs:label "Membrane ultrarapid delayed rectifier potassium current conductance scaling factor" ;
rdfs:comment "A scalar that multiplies the conductance term for this current" .
# I_Kss or Iss
:membrane_non_inactivating_steady_state_potassium_current
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :IonicCurrent ;
rdfs:label "Membrane non-inactivating steady-state potassium current" .
:membrane_non_inactivating_steady_state_potassium_current_conductance
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane non-inactivating steady-state potassium current conductance" .
# I K1
:membrane_inward_rectifier_potassium_current
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :IonicCurrent ;
rdfs:label "Membrane inward rectifier potassium current" .
:membrane_inward_rectifier_potassium_current_conductance
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane inward rectifier potassium current conductance" .
:membrane_inward_rectifier_potassium_current_conductance_scaling_factor
a :Annotation ;
a :MembranePotassiumChannelRelated ;
rdfs:label "Membrane inward rectifier potassium current conductance scaling factor" ;
rdfs:comment "A scalar that multiplies the conductance term for this current" .
# I to, (a.k.a. I_to1) sometimes fast and slow components, sometimes not.
:membrane_transient_outward_current
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :IonicCurrent ;
rdfs:comment "I_to is a potassium current, sometimes subdivided into fast and slow components (a.k.a. I_to1)" ;
rdfs:label "Membrane transient outward current" .
:membrane_transient_outward_current_conductance
a :Annotation ;
a :MembranePotassiumChannelRelated ;
a :ConductanceOrPermeability ;
rdfs:label "Membrane transient outward current conductance" .
:membrane_transient_outward_current_conductance_scaling_factor
a :Annotation ;
a :MembranePotassiumChannelRelated ;