Tag: Semantic Web

The Whole Brain Catalog is the Google Earth for the brain. Unlike the earth, however, there isn’t just one brain. There are any number of variations found across the brains of individuals and, of course, there are major differences between brains across species. For that reason alone, the “typical” mouse brain that the Whole Brain Catalog offers is just a start. It’s an impressive beginning.

There is a lot to explore in the Whole Brain Catalog so I’ll only attempt to introduce you to it here. Over the days to follow I’ll be highlighting different aspects of this important tool.

Running the Whole Brain Catalog requires Java, a good Internet connection, and a relatively powerful computer. Most recently purchased laptop and desktop computers should run it just fine. Check out the requirement specifics and download the application from the Whole Brain Catalog Download Page.

Note: Whole Brain Catalog is currently in what I’d call the alpha stage. Be prepared for some bumps.

When the three dimensional mouse brain appears I recommend clicking on the “Rotate Camera” button above the brain and towards left and then grabbing onto the brain and rotating it around. Do this by pointing to the brain, holding down your mouse button, and moving the mouse. This should help orient you.

Note: Do not click on the maximize window button and beware of resizing the window by dragging its corner. On my Macintosh running the latest version of OSX and Java this causes the computer to be completely inaccessible to me (including the Whole Brain Catalog). [Sometimes this happens and sometimes not. I haven’t been able to isolate the problem yet. Please post and let me know if you figure it out.]

While rotating the brain I found it helpful to zoom it out some (make it smaller). Click on the “Zoom Out” button above the brain and about in the middle. Then point to the brain, double click your mouse button and hold the button down on the second click. The brain will zoom out relatively fast as long as you hold the button. (Press once on your mouse button and hold to zoom slower. Use this when you’re working at a smaller scale like looking at single neurons.) Use the “Zoom In” button to the left of the “Zoom Out” button in the same way except that the brain will get larger.

Once you’re oriented to the brain, check out how fun it is to fly around and explore brain anatomy. By default only a subset of “Brain Regions” and “Mesh Model” data are loaded. You can see the available data and data that has been selected to view in the area titled “Data Type” to the left of the brain viewer and at bottom.

The default selections don’t come close to all of the data available even within these two high level categories. Keep in mind that the more data selected the longer it takes to download from the Internet. Also, with more data to handle, your computer may slow down significantly. Also take into account that the amount of data visible all at once on your screen may become overwhelming.

Leave the settings on default for now and move your pointer over the brain. Notice the label changing at the lower left in the brain viewing area? This label displays the name of the brain structure that your mouse pointer is flying over.

Click on the “Zoom In” button and double click and hold over the tangle of red (lateral geniculate body, optic tract) inside the brain. You can get close up and personal with brain structures.

Tomorrow I’ll write about some of the data associated with these structures that you can work with and view. Meanwhile have fun exploring the Whole Brain Catalog, which may become the hub for accessing the broad range of brain relevant data distributed in repositories across the Internet.

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