NeuronDB FAQ
Version 5.0 – Update January 04, 2000.
Welcome to the new improved version of
NeuronDB. Since the last version NeurondDB 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has been replaced by the more accurate term "data".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
"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."
This
site is ©
Copyright 2000, Shepherd Lab, Yale University. All rights reserved.
|
|