Browse NeuronDB in NIF
For more information, visit NeuronDB Homepage or the NeuroLex entry for NeuronDB
NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.
This tool should be used to determine if evidence exists for a particular current or transmitter in a cell type.
From the NIF interface, we can start by searching for our favorite cell. Note, the autocomplete feature of NIF helps identify cell types that NIF knows about. It is good to use autocompleted terms when applicable. Here we start typing in purkin and autocomplete to "Purkinje Cell"
The "Purkinje Cell" query brings up many results from NeuronDB: Currents in the Cellular Level tab. See the results below:
The user should be able to see which currents are present or absent in which compartment of the cell.
Navigating to the cerebellar purkinje link, takes user to NeuronDB with a wealth of data gathered from published work for cerebellar purkinje cells, including information about intrinsic currents, connectivity data, dendritic fields, receptors, channels, neurotransmitters as well as genes and chromosome data.
Note, clicking on the tabs for the mode, region, properties, and interoperation gives different sets of data about cerebellar purkinje cells.
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 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 compartment.
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 compartment.
- 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 this compartment.
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 of properties.
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 property.
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 results, etc.
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 Mode.
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.