NeuronDB FAQ

Version 5.0 – Update January 04, 2000.

    Welcome to the new improved version of NeuronDB. Since the last version NeuronDB database has been modified to interoperate with the new cellular properties database (CellPropDB).

Version 4.0 – Update April 29, 1999.

    As a user you will benefit from a new look for the data pages, in which the former terminology of "terse" has been replaced by the more accurate term "data". Use this first to identify the data in which you are interested, then go to "data plus connections" to identify the synaptic inputs and outputs, then "data plus references/notes" for full citations with commentaries. As a user you will not see directly the considerable work that has gone into reformatting into what is called an "EAV" (entity-attribute-value) database structure, but you will benefit from it by faster operation and by our ability to add new features in an efficient manner. There is also a simpler page for enabling users to input new data or provide commentaries or corrections. Please use this page or continue to communicate with us through email to upgrade the data already in the database of suggest new neurons to include.

Version 3.0 – Update Jan 20, 1998

    Since last May we have been working to improve NeuronDB in two ways. First is to input more data for the different neurons. Progress has been made especially with regard to pyramidal neurons in CA1 and CA3 of the hippocampus and the superficial and deep pyramidal neurons of the cerebral cortex. We thank John McGann for his outstanding contribution in obtaining these data and references, and entering them into the database. Second, the database is in process of been reformatted into a more robust type of database structure called entity attribute value (EAV) design. This will enable new types of properties and neuronal relations to be implemented much more efficiently. A new version incorporating these changes will be available within a few weeks.

Version 3.0 - released May 1, 1998

    This version provides properties plus annotations for all of the cells in database. In addition, we are introducing an interface to a new companion database of published compartmental models, termed ModelDB. Users are encouraged to contribute properties and annotations wherever appropriate. In order to facilitate use of the database, access has been streamlined so that viewing the database and inputting data can be done directly by all users.

Why was NeuronDB built?

    Understanding the significance of a specific property at a specific site requires relating that property to the integrative context of that neuron, and comparing it with other neurons. NeuronDB is a tool which allows the comparison of compartmentalized neurons in a number of different ways. NeuronDB will allow its users to gain a deeper understanding of the membrane properties of neurons across the nervous system. NeuronDB is one in a cluster of databases that are part of the SenseLab Project.

What type of problems can NeuronDB help me solve?

    NeuronDB tracks three different types of membrane property data: receptors, channels, and transmitters. Users can solve questions of what types of properties are located within a specific compartment of a specific neuron. Or users may take the opposite route and solve questions of which neurons contain a specific property. Within the data pages are links which allow comparisons of related neurons or properties. References are provided for much of the data found in NeuronDB as well as a direct link to the appropriate medline abstract where available.

How is NeuronDB organized? How do I use NeuronDB?

    Currently, NeuronDB has four routes to view the data. To look at neurons and view what properties are contained within the neuron, choose the "Compartmentalized Neurons" link on the home page. To view a list of currents, receptors, or neurotransmitters and find out where they are located within the neurons in the database, choose the appropriate link from "Properties: Currents or Neurotransmitters and Receptors" on the home page. To view the database through generic compartments, click on "Canonical forms." Or to select a reference and view data which has been extracted from that reference, choose "Bibliographic searches." Subsequent links are explained on the pages on which they appear. Clicking on the NeuronDB banner will always bring you back to the home page. The up arrow in the top left hand corner of every page (except the home page), takes you up one level of the database heirarchy in the context of where you currently are located. The file folders of properties change your context from one property to another.

    It is the intention that every property in NeuronDB will be supported by annotations with full literature citations. To achieve this goal, it will be important for users to contribute to the properties and annotations.

Who can use NeuronDB?

    The use of NeuronDB is not restricted; it is open to all viewers. Users are encouraged not only to view the data but also to submit wherever appropriate.

Technically, what is going on here?

    NeuronDB is a publicly accessible web project. It is housed on a NT 4.0 server and uses Oracle 7.3 as its database management software housed remotely in a Unix machine. Most of the pages of NeuronDB are generated "on the fly" by CGI programs written in ASP - VBScript.

What do all of these abbreviations stand for?

    All of the neurons in the database fall within one of three canonical forms. A canonical form contains the least number of compartments while still representing neuronal structure and function (Shepherd 1992). These forms are based on Rall's (1959) method of collapsing all of the dendrites in the dendritic tree into an equivalent cylinder, and the adaptation of this approach to generate an equivalent dendrite (Rall and Shepherd, 1968).

    Form 1: Sensory cell with cilia

      Dc - Dendritic cilia
      S - Soma

    Form 2: Cell with single dendrite or multipolar cell

      Ded - Distal equivalent dendrite
      Dem - Middle equivalent dendrite
      Dep - Proximal equivalent dendrite
      S - Soma
      AH - Axon Hillock (plus initial segment)
      A - Axon
      T - Terminus

    Form 3: Cell with apical and basal dendrites

      Dad - Distal apical dendrite
      Dam - Middle apical dendrite
      Dap - Proximal apical dendrite
      Dbd - Distal basal dendrite
      Dbm - Middle basal dendrite
      Dbp - Proximal basal dendrite
      S - Soma
      AH - Axon Hillock (plus initial segment)
      A - Axon
      T - Terminus

What is the Human Brain Project?

    "The Human Brain Project is a broad-based long-term research initiative which supports research and development of advanced technologies to open information superhighways to neuroscientists and behavioral scientists by providing an array of information tools for the 21st Century."

What is SenseLab?