Database tools for integrating and searching membrane property data correlated with neuronal morphology.
A critical problem in neuroscience is the lack of database tools for integrating neuronal property data. We report here the development of a combined object oriented-relational database (NeuronDB, http://senselab.med.yale.edu/neurondb) that meets these needs by providing tools for integrating data within neurons and comparing data across neurons. It focuses on three types of neuronal properties voltage-gated channels, neurotransmitter receptors, and neurotransmitters. The data are organized in relation to different regions of neurons as represented in canonical forms; using simple canonical models of complex cells as a vehicle for indexing information permits the database to be searchable across different neurons. Using these multidimensional search tools, users can locate specific properties in specific regions of a neuron; obtain integrated summaries of all properties within a region; and carry out searches to compare properties across equivalent compartments in different neurons. These tools thus permit searches of the multidimensional neuron property space equivalent to homology searches of sequence databases. NeuronDB is accessible over the Internet; it provides immediate links to citation indexes and abstracts supporting the deposited data, and annotations that indicate the state of acceptance of the data. Users are encouraged to contribute data. The ability to input the data from NeuronDB directly to NEURON and GENESIS is being developed. As a shared Web resource, NeuronDB should enhance the efforts of neuroscientists and neuronal modellers to analyze and compare the functional operations of different types of neurons.
Mirsky
J S
JS
Section of Neurobiology, Yale University School of Medicine, New Haven, CT 06510, USA. jason.mirsky@yale.edu
Nadkarni
P M
PM
Healy
M D
MD
Miller
P L
PL
Shepherd
G M
GM
D001331:Automation; D016208:Databases, Factual; D003712:Dendrites / Q000648:ultrastructure; D015640:Ion Channel Gating; D008564:Membrane Potentials / Q000502:physiology; D009474:Neurons / Q000648:ultrastructure*; D018377:Neurotransmitter Agents / Q000378:metabolism; D010865:Pilot Projects; D015203:Reproducibility of Results
D018377:Neurotransmitter Agents