Tools for Searching for Neuron Properties in NeuronDB
This is a summary of the main kinds of tools that are available to the user
for identifying different types of membrane properties and their functions in
different neurons and their compartments.
Search for a neuron
Enter the database through Neuron List or Neuron List by Brain
Select neuron of interest, either Principal neuron or Interneuron
within a given brain region.
Search for the membrane properties of a neuron
Problem: We wish to know what are the membrane
properties of different parts of a particular type of neuron.
The main page for a neuron type shows a Golgi-stained neuron with different
compartments labelled, together with a canonical representation. See the legend
below for the key to the abbreviations.
Search Procedure: To search for membrane properties, Set Mode
to Data/Search. (The default settings will show, under Region, All
Compartments, and under Properties, All Properties.)
Data/Search gives an overview of the membrane properties found in all
compartments in this neuron.
...Plus Connectivity shows the membrane properties plus synaptic
connections to all compartments in this neuron.
...plus References/Notes gives comments and citations to the literature
for all properties of all compartments in this neuron.
(Select Models to go to ModelDB; see below)
Results: The search enables the user to: observe the
combination of membrane properties that mediates the integrated activity of a
given compartment; compare the combinations of properties in different
compartments; identify the series of papers that has established a property in
a compartment of this neuron type; and learn of controversies about the
evidence for particular properties as a stimulus to further research.
Analyse the membrane properties in a specific compartment
Problem: We wish to focus on membrane properties in a given
Search Procedure: Select for Mode of display. Use
default settings as above and scroll to desired compartment. Alternatively,
under Region, select one of the canonical compartments as represented in
the diagram. Alternatively, under Properties, select for Receptors,
Channels, Transmitters, or All Properties.
Results: As in (2) above, but with the focus on a single
Compare single properties between neurons and compartments
Continue with (2) and (3) above by selecting an individual membrane
property in one of the compartments (e.g., I Na,t) and keying the Search
button at the bottom of the page..
This will give a list (Neurons having the selected properties in their
specific compartments) of all other neurons that have this property in
It will also show (in pink) neurons that are known not to have this property in
that compartment. Neurons not on this list are not known to have or not to have
this property, i.e. no information is available regarding this property in this
compartment in this neuron.
Select corresponding to expand the list to show the corresponding
compartments in all canonical representations (i.e., distal apical dendrite
(Dad), distal basal dendrite (Dab) and distal equivalent dendrite (Ded)) that
have, or not to have, this property.
Select all to expand the list to include all compartments in all neurons
that have been shown to have, or not to have, this property.
Compare multiple properties between neurons and compartments
Problem: We want to search for an arbitrary set of properties
across all neurons.
Search Procedure: Select Data/Search; enter checks in
boxes for the desired properties. At bottom of page, select for search in
the compartments in that precise type of dendrite (specific compartment)
or the compartments in all types of dendrite (corresponding
compartments). Then hit search to obtain all compartments with this set
Results: The search is similar to a blast search of a
sequence database to give all sequences with a particular motif. This
unique tool enables the neuroscientist to conduct an analogous search for the
motif of membrane properties that is common to the compartments of different
types of neurons.
Navigate between neurons by means of Connectivity
Problem: How do we identify the membrane properties related to the
connectivity between neurons?
Search Procedures: The neurons can be searched by means of
their synaptic connectivity.
In the plus Connectivity mode, selection of a receptor in a
compartment also gives the presynaptic source of the transmitter acting on that
receptor, which can be selected in order to search the presynaptic neuron.
Similarly, selection of an output transmitter from a compartment (right hand
column) gives the postsynaptic neuron, which can be selected and searched.
Results: This search tool enables the user to navigate quickly
from one neuron to the next.
Verify properties by citations
Problem: What is the documentation for a given property in a given
compartment in a given neuron type?
Search Procedure: In the plus References/Notes Mode,
references are cited which have established the presence or absence of a given
The references are listed at the bottom of the page. Selecting a reference
brings one directly to PubMed and the article.
Results: Complete documentation for a given property is
provided, where also will be found the details of the density, kinetic
properties, etc, as well as notes on controversial aspects of the data.
Assess data quality and significance by the Plus References/Notes
Problem: Much neuroscience data is qualified by technical aspects,
such as species, age of animals, types of instrumentation, reproducibility of
Search Procedures: In the plus References/Notes Mode,
references provide annotations with commentaries on these questions.
Results: The annotations and commentaries enable the user to
assess the significance of each paper and their relevance for including a given
property in computational simulations of the experimental results.
Incorporate the membrane properties in computational simulations
Problem: How can one readily access compartmental models to aid in
the analysis of the integrative activity of the membrane properties of a given
type of neuron?
Search Procedures: The database in NeuronDB provides a
resource for building the appropriate membrane properties into the model to be
constructed and tested. To go to the model database to determine which models
are most relevant to the users needs and interests, select Models under
Results: The direct connection between NeuronDB and ModelDB
provides a seamless interface between experiment and theory in analysing
neuronal properties and understanding how they are integrated to mediate the
functions of the neuron.
Check also NeuronDB FAQs