Tritonia Ontology

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This provides definitions for the objects, attributes, and attribute values in the Tritonia ontology used in NeuronBank.

These are major Object Classes: Annotations, Connections, Neuron.

All NeuronBank Objects have Annotations and AccessionIDs. In addition, there are class-related properties. See NeuronBank Help / Core Ontology and Ontology editing

Annotations

All objects can have relationships to Annotations.

Reference

This can be an Article, Book, Book Chapter, or Conference Abstract

Link

These are hyperlinks to sites on the web. In NeuronBank, they are clickable.

Comment

This is a text string.

Example

This is a jpeg file.

Revision

Not used yet. The intent is to be able to keep track of versions.

Contributor

This is the person who contributed the information to the database.

Connections

Only a Neuron has Connections. There are four subclassifications of Connections:

  1. Chemical Synapse
  2. Electrical Synapse
  3. Negative Connection
  4. Modulation

Extensible attributes that apply to Chemical Synapse, Electrical Synapse and Modulation:

  • -Laterality: A neuron connects with another neuron in one of three configurations:
    1. Bilateral - the connection is between the neuron and specificed neurons on both sides of the midline.
    2. Ipsilateral - the connection is between the neuron and specificed neurons only on the same side of the midline.
    3. Contralateral - the connection is between the neuron and specificed neurons only on the opposite side of the midline.
    4. Unspecified - the laterality of the connection is not known.
    • Note that the location of the neurons are defined by the location of the cell soma, not the physical location of the contact point between the neurons.

Chemical Synapse

A Chemical Synapse is a connection from one neuron (presynaptic) to another neuron (postsynaptic) that involves the use of a neurotransmitter and produces a measurable change in post-synaptic membrane potential.

Extensible attributes:

  • -Laterality: see definition in Connections
  • -Connection_Probablity: The probability of a functional synapse between exemplars of the pre- and post- synaptic neuron types expressed as percent. Must be whole number.
  • -Reversal_Potential: The membrane potential at which the synaptic current reverses from inward to outward. Units: mV
  • -Molecule: The molecule contained used at the synapse as determined by immunohistochemistry, pharamcological, or other analytical techniques.
    • Expandable category. Current values:
      • 5-HT: Serotonin, 5-hydroxytryptamine
      • Peptide-unidentified: uncharacterized peptide
      • GABA: gamma-amino butyric acid
      • Glutamate
    • Also applies to Modulation and Neuron
  • -Short_Term_Plasticity: Changes in synaptic strength during trains of stimuli.
    • Categorical
      • Depressing - overall trend is for the synaptic strength to get weaker with repetition
      • Facilitating - overall trend is for the synaptic strength to get stronger with repetition
  • -Synaptic_Component: Chemical synapses can have multiple components
    • Categorical:
      • Excitatory - EPSP with time course not described
      • Inhibitory - IPSP with time course not described
      • Excitatory - Fast : rapid EPSPs
      • Excitatory - Slow: Non distinct EPSPs, time constant of decay > 1sec
      • Inhibitory - Fast: rapid IPSPs
      • Inhibitory - Slow: Non distinct IPSPs, time constant of decay >1 sec
  • -Monosynapticity: Describes whether a chemical synapse has been shown to be monosynaptic, polysynaptic.
    • Categorical
      • monosynaptic - There is a direct connection from the presynaptic neuron to the post-synaptic neuron.
      • polysynaptic - The effect of the presynaptic neuron on the postsynaptic neuron is mediated by an intervening neuron. Generally, when this is shown the intervening neuron has not been identified.
      • unkown

Electrical Synapse

An Electrical Synapse is a connection from one neuron to another neuron that involves direct transfer of electrical charge (usually mediated by gap junctions).

Extensible attributes:

Negative Connection

A negative connection is meant to mean that it is established that no connection exists between these two neurons. This is distinct from the extensible attribute -Connection Probability

Modulation

Modulation represents a neuromodulatory connection from one neuron to another neurons that does not necessarily result in a change in membrane potential but does cause a change in the properties of the post-synaptic neuron or its synapses.

Extensible attributes:

  • -Laterality: see definition in Connections
  • -Molecule: The molecule contained used at the synapse as determined by immunohistochemistry, pharamcological, or other analytical techniques.
    • Expandable category. Current values:
      • 5-HT: Serotonin, 5-hydroxytryptamine
      • Peptide-unidentified: uncharacterized peptide
      • GABA: gamma-amino butyric acid
      • Glutamate

Neuron

Neurons can be individual cells or members of a cluster.

Core attributes of Neurons

Fig. 1 Drawing of Tritonia central ganglia
  • Soma location in the Tritonia Central Ganglia.
    • Ce = Cerebral ganglion
    • Pl = Pleural ganglion
    • Pd = Pedal ganglion
  • The location is displayed on a standardized map with a grid. The map is bilaterally symmetric on the cerebral commissure.

Extensible attributes of Neurons

  • -V_Rest = Resting membrane potential
    • numeric value, units millivolts (mV)
  • -Cell_Count = number of neurons in that category of neuron
    • numberic value, no units.
    • This applies unilaterally. Thus DSI has a cell count of 3 because there are 3 on each side of the brain.
  • -Input_Resistance = measured when the neuron is at rest, this is the voltage divided by a small current (typically -1nA).
    • numeric value, units MegaOhms
  • -Soma_diameter = The diameter of the soma in an average adult specimen.
    • numeric value, units microns
  • -Activity_Resting = Describes the electrophysiological activity of a neuron recorded with no stimulation.
    • Categorical
      • Silent = Neuron is generally silent at rest.
      • Spiking = Neuron generally shows tonic spiking.
      • Bursting = Rhythmic bursting is typical.
      • Irregular = Spontaneous activity that has burst-like qualities but has complex rhythmicity.
  • -Behavior = The behaviors that this neuron has been directly associated with producing
    • Categorical
      • Withdrawal = of body wall
      • Arousal = activates crawling
      • Branchial_Tuft_Withdrawal = withdrawal of gills
      • Body_Flexion = bending the body
      • Feeding = Anything associated with feeding
      • Swimming = rhythmic dorsal-ventral body flexions
      • Ciliary locomotion = crawling via cilia on the foot
  • -Molecule: The molecule contained used at the synapse as determined by immunohistochemistry, pharamcological, or other analytical techniques.
    • Expandable category. Current values:
      • 5-HT: Serotonin, 5-hydroxytryptamine
      • Peptide-unidentified: uncharacterized peptide
      • GABA: gamma-amino butyric acid
      • Glutamate
    • Also pertains to Chemical Synapse and Modulation
  • -Nerve_Projection = Neuron known to have a process in the given nerve through appearance of antidromic spike during nerve stim, or by backfill of that nerve labeling the soma, or by intracellular dye injection showing an axon in that nerve.
    • Categorical (see Fig 1 diagram of Ganglion)
      • CeN1-6 = Cerebral Nerves 1,2,3,4,5,6
      • PdN1-6 = Pedal Nerves 1,2,3,4,5,6
        • Pedal Nerves 5 and 6 are Pedal-Pedal commissures
      • PlN1-3 = Pleural Nerves 1,2,3
      • CeC = Cerebral Commissure
      • CePdC = Cerebral-Pedal Connective
  • -Neuron_Type = Broad category of neuronal types:
    • Categorical
      • Interneuron = does not leave central ganglia
      • Motor Neuron = axon exits through body wall nerve and causes motor response
      • Sensory Neuron = has dendrite or axon in body wall nerve and carries afferent information
      • Undetermined = not known
  • -Soma_Coloration = Cell body coloration as viewed in reflected white light through a dissection microscope in an unfixed preparation.
    • Categorical
      • White
      • Clear
      • Orange
      • Reddish
      • Brown
  • -Soma_Laterality = The presence of the same neuronal class either unilaterally or bilaterally in the brain.
    • Categorical
      • Left - present only on left side of the brain.
      • Right - present only on right side of the brain.
      • Bilateral - present on both sides of the brain.
  • -Swim_Phase = Phase of escape swimming during which the neuron is active. The swim consists of alternating dorsal-ventral flexions.
    • Categorical
      • Dorsal - active during the dorsal flexion phase
      • Ventral - active during the ventral flexion phase
      • Constant Activation - active constantly, not rhythmic during swim motor pattern
      • None - No activity during swim motor pattern
      • Overlapping - bursts do not correspond to dorsal or ventral phases
  • -Spike_Frequency_Adaptation = The extent to which spike rate decreases with constant current injection.
    • Categorical
      • Strong - Greatly than 50% decrease in spike frequency at the end of a 2 sec current pulse
      • Weak - Noticeable decrease in spike frequency, but less than 50% decrease
      • None - Same frequency at beginning and end of current pulse
  • -Swim_Burst_Class = classification of swimming bursts by Hume et al. 1982 (ID Tri0002275). In this paper, the authors define 6 classes of bursting in swim neurons:
    Tritonia burst types
    • Quoted from paper:
      • a) high-frequency bursts, symmetrical around their peak, with a rapid rising phase and a rapid falling phase
      • b) high-frequency bursts, asymmetrical around their peak, with a slow rising phase and a rapid falling phase
      • c)high-frequency bursts, asymmetrical around their peak, with a rapid rising phase and a slow falling phase
      • d) high-frequency bursts, symmetrical around their peak, with a slow rising and slow falling phase;
      • e) low-frequency bursts;
      • f) bursts with two frequency peaks. In cells with type f bursts, both frequency peaks occurred during a single flexion phase of the swim cycle, and the bursts are continuous. The pattern of activity in these cells thus differs from that in the class III and IV cells, which have one burst in each flexion phase separated by an interburst interval.
  • -conductance_types = conductance types found in a neuron. Determined by voltage clamp or pharmacology.
    • Categorical
      • A-Current - Transient, voltage-dependent outward current
      • H-Current - Hyperpolarization activated inward current
      • L-type Calcium - Low threshold calcium current