NeuronBank: Neuronal Circuit Online Data Repository

The neuron doctrine has been central to neuroscience for more than a century with the idea that the neuron (the individual brain cell) is the fundamental building block of the brain. Ramon y Cajal, the originator of the neuron doctrine, began classifying neurons based on cell shape and connectivity. Ramon y Cajal suggested that a relationship exists between a neuron’s shape, the connections (synapses) it receives and the synapses it makes with other neurons, and the neuron’s function.

Individual neurons are connected by synapses into functional units known as neuronal circuits. We may consider neuronal circuits as the fundamental units underlying signal processing (information processing) in the brain.

A recent paper describes an online data repository called NeuronBank that is focused on neurons and the neuronal circuits they participate in. The paper “NeuronBank: a tool for cataloging neuronal circuitry” was published April 19, 2010 in Frontiers in Systems Neuroscience.

Classifying neurons is far from straight forward and identifying the neuronal circuits they participate in is even more difficult. This is true for even the simplest animals with nervous system. Nevertheless, the problem is relatively more tractable in invertebrate nervous systems where individual neurons can be uniquely identified and have similar properties from animal to animal, which isn’t true in vertebrate nervous systems.

In some invertebrate animals it is possible to identify every neuron in the nervous system, as has been done for a worm (Caenorhabditis elegans) which has precisely 302 neurons. The online data repository WormAtlas.org includes data on all of the worm’s neurons along with their synaptic connections, gene expression profiles, anatomy, neurotransmitters, and developmental lineage.

The team that created the NeuronBank decided to start with animals that were more complex than the worm but far simpler than vertebrates. They focused on the nervous systems in gastropod molluscs, which have around 8,000 to 10,000 neurons. Individual neurons and classes of neurons can be identified along with neural circuits underlying specific behaviors.

NeuronBank was designed to use terminology commonly agreed upon by the community of users. NeuronBank uses a two part hierarchical ontology to represent the knowledge about neurons and connections: (a) a core ontology applicable across species, and (b) an extensible list of attributes that can be tailored for a specific species. Their ontology appears to follow Semantic Web standards.

Currently NeuronBank contains data from two invertebrate species. The site is in what I’d call an early alpha version (proof of concept). If you’d like to try it out I suggest going to the paper and following the “An Example Search” section under “Results.” It looks like the site only works with Firefox and visualization doesn’t seem to work at all. There is supposed to be a LocationVis plug-in that I was unable to find and nothing showed up.

Clearly when I look up, for instance, a Purkinje cell I should be one link away from information on the circuit or circuits that the cell type is involved in. The NeuronBank team has made a commendable start on a neuron and neuronal circuit repository that may be integrated into the global neuroscience knowledge base.

Other related blog posts:

Brain Research Using Online Data Repositories: Network Structure of the Brain

Brain Research Using Online Data Repositories: Brain Cell Shape and Function