Ontology terms for ionic currents

No adequate ontology has been found for describing the various ionic currents used in the literature. We therefore used different sources to defined such an ontology. Here is the hierarchy of ionic currents established so far:

 

• Transmembrane ionic current
  • Sodium current
    • Sodium leak current
    • Sodium transient fast current
    • Sodium transient slow current
    • Sodium pesistent current
  • Excitatory postsynaptic current
  • Inhibitory postsynaptic current
  • Non-selective current
    • Calcium activated nonspecific cation current
    • Cyclic-nucleotide gated nonspecific cation current
      • Inward rectifier (h-type) current
  • Choride current
    • GABA-related cloride current
    • Calcium activated chloride current
  • Potassium current
    • Calcium-dependent potassium current
      • Fast voltage- and calcium-dependent potassium current
      • Slow calcium-dependent AHP potassium current
      • Medium calcium-dependent AHP potassium (SK) current
    • A current
      • I A, slow
    • Potassium delayed rectifier
    • Potassium leak current
    • M-type potassium current
    • Potassium inward rectifier (Kir) current
    • Fast voltage-gated potassium (Kf) current
  • Calcium current
    • Low threshold calcium T-current
    • Slow high threshold calcium current
    • q- and p-type calcium current
    • N-type calcium current
  • Leak ionic current

     

This hierarchy tries to take into account currents as described in different publications as well as tags already available in the Knowledge-space.org ontology and the NeuronDB site.

 

Standard current terms from Knowledge-space:

Label	ID	Definition
Transmembrane ionic current	NIFMOL:nifext_8054	The disposition of cellular membrane to support ionic current flow primarily via membrane spanning macromolecules or channels whose conductance is ion-selective and dependent on ionic, chemical, and/or electronic environment.
Sodium current	NIFMOL:nifext_8055
Excitatory postsynaptic current	NIFMOL:nlx_mol_100201	Any synaptic current which increases the likelihood of an action potential firing. Typically this is mediated by an increase in sodium or calcium conductance or a decrease in potassium conductance. It is usually synonymous with an evoked excitatory post synaptic current., Any synaptic current which increases the likelihood of an action potential firing. Typically this is mediated by an increase in sodium or calcium conductance or a decrease in potassium conductance. It is usually synonymous with an evoked excitatory post synaptic current., Any synaptic current which increases the likelihood of an action potential firing. Typically this is mediated by an increase in sodium or calcium conductance or a decrease in potassium conductance. It is usually synonymous with an evoked excitatory post synaptic current.
Inhibitory postsynaptic current	NIFMOL:nlx_mol_100202	Any synaptic current which reduces the likelihood of an action potential. Typically this is mediated by an increase in chloride conductance or potassium conductance. Inhibitory postsynaptic current is usually synonymous with an evoked inhibitory post synaptic current. , Any synaptic current which reduces the likelihood of an action potential. Typically this is mediated by an increase in chloride conductance or potassium conductance. Inhibitory postsynaptic current is usually synonymous with an evoked inhibitory post synaptic current., Any synaptic current which reduces the likelihood of an action potential. Typically this is mediated by an increase in chloride conductance or potassium conductance. Inhibitory postsynaptic current is usually synonymous with an evoked inhibitory post synaptic current.
Non-selective current	NIFMOL:nifext_8059
Choride current	NIFMOL:nifext_8058
Potassium current	NIFMOL:nifext_8056
Calcium-dependent potassium current	NIFMOL:nifext_8060
A current	NIFMOL:nlx_mol_20081201	"Transient"; inactivating potassium current, involved in delayed onset of firing; interspike interval; action potential repolarization.
I A, slow	NIFMOL:nlx_mol_20081202	Slowly inactivating \"delay\" potassium current I K(D), similar to the A-type current but inactivates slowly (seconds). Participates in spike repolarization.
Calcium current	NIFMOL:nifext_8057

 

Supplementary terms created "in-house" for annotating the literature:

Label	ID	Definition
Leak ionic current	BBP_nlx_0001	General leaking ionic current
Sodium leak current	BBP_nlx_0002	Sodium leaking ionic current.
Sodium transient fast current	BBP_nlx_0003	Fast, transient, inactivating sodium current [NeuronDB: I Na,t].
Sodium transient slow current	BBP_nlx_0004	Slow, transient, inactivating sodium current.
Sodium pesistent current	BBP_nlx_0005	Persistent (or noninactivating) sodium current [NeuronDB: I Na,p].
Potassium delayed rectifier	BBP_nlx_0006	Delayed rectifier, slowly inactivating or non-inactivating [NeuronDB: I K].
Potassium leak current	BBP_nlx_0007	Potassium leaking ionic current [NeuronDB: I K,leak].
M-type potassium current	BBP_nlx_0008	Muscarinic receptor-suppressed potassium current [NeuronDB: I M]
Fast voltage- and calcium-dependent potassium current	BBP_nlx_0009	Fast voltage- and [Ca2+]-dependent potassium current [subclass of NeuronDB I K,Ca].
Slow calcium-dependent AHP potassium current	BBP_nlx_0010	Slow [Ca2+]-dependent, afterhyperpolarization potassium current [subclass of NeuronDB I K,Ca].
Low threshold calcium T-current	BBP_nlx_0011	Low-threshold inactivating, transient calcium current. Blocked by the non-specific channel blocker Ni2+ [NeuronDB: I T low threshold].
Slow high threshold calcium current	BBP_nlx_0012	High-threshold slow or non-inactivating calcium current. L-type current. Also known as the dihydropyridine channel, or DHP channel. This channel has four subunits: Cav1.1, Cav1.2, Cav1.3, Cav1.4. Blocked by nimodipine. [NeuronDB: I L high threshold]
q- and p-type calcium current	BBP_nlx_0013	Includes both p-type and q-type calcium currents [NeuronDB: I p,q].
N-type calcium current	BBP_nlx_0014	Rapidly inactivating calcium current with threshold around -20 mV. Underlies Ca2+ spikes that are prominent in dendrites. Involved in synaptic transmission [NeuronDB: I N].
Calcium activated chloride current	BBP_nlx_0015	Calcium activated chloride current. Can enhance or decrease response depending on the Cl- equilibrium potential [NeuronDB: I Cl,Ca].
Calcium activated nonspecific cation current	BBP_nlx_0016	Calcium Activated Nonspecific cation current [NeuronDB: I CAN].
Cyclic-nucleotide gated nonspecific cation current	BBP_nlx_0017	Cyclic-Nucleotide Gated nonspecific cation channel [NeuronDB: I CNG].
Inward rectifier (h-type) current	BBP_nlx_0018	Inward rectifier ('Queer'), activated by hyperpolarization, cyclic-nucleotide gated mixed cation current. Prevents strong hyperpolarization; increases membrane resistance during membrane depolarization [NeuronDB: I h]. See (Luthi and McCormick, 1998, Neuron, pp.9-12)
Potassium inward rectifier (Kir) current	BBP_nlx_0019	Potassium inward rectifier activated by hyperpolarization. [included in I h in NeuronDB]. See (Lee and Ishida, 2007, J Neurophysiol, pp.3790-9)
Fast voltage-gated potassium (Kf) current	BBP_nlx_0020	Fast voltage-gated potassium current. See (Kang, Huguenard and Prince, 2000, J Neurophysiol, pp.70-80)
Medium calcium-dependent AHP potassium (SK) current	BBP_nlx_0024	Apamin-sensitive SK (Small-K+ conductance) current causing medium (vs. slow or fast) AHP.
GABA-related cloride current	BBP_nlx_0027	Chloride current through GABA_A receptor.