NIF: Neurons, Models, and Grants

Yesterday we took an initial peek at the Neuroscience Information Framework (NIF). Today I’d like to briefly point to the range of Data Federation resources you can find there. When “barrel cortex” is typed into the NIF search box and a search is executed, a couple of subcategories come up under the Nervous System Level category and about five subcategories under Data Type like in Figure 1 below.

NIF search results for 'barrel cortex'.
Figure 1. NIF search results for “barrel cortex.” The search words refer to whisker related structures in layer 4 of somatosensory cortex.

In Figure 1 above, the NeuroMorpho: NeuronInfo entry under the Cellular Level subcategory is selected which results in showing a list of some of the 66 neurons from the repository that are associated with the barrel cortex.

A section from a mouse brain in
Figure 2. A section from a mouse brain in The barrel cortex is labeled “barrels” in red with yellow background.

Click on the plus (+) sign to the right of Brain Regions to display entries in that subcategory. The BAMS: BrainRegions entry is associated with an anatomy ontology that provides standard naming conventions for brain structures. The BrainMaps:Atlas entry provides access to relevant high-resolution histology sections. Click on the barrel cortex, barrels link under Brain Region and the atlas will appear like in Figure 2 above.

Under the Data Type category, the Images subcategory lists the sites we’ve already looked at. The Models subcategory lists computational model sites relevant to our search. The ModelDB: Models entry lists three models of barrel cortex in the SenseLab ModelDB repository.

You may be puzzled why the Grants subcategory under Data Type shows large number of hits (73 while writing this) but the Grants tab at the top of the section has none. The Grants subcategory provides access to resources on past and currently funded grants. In contrast, the Grants tab provides resources for those wanting to apply for federally funded grants.

Yesterday we looked at resources available under the Microarray subcategory. Our current search brought up 1 resource at the Gene Expression Omnibus (GEO). Finally, under Connectivity you will find information on the known neural connections to and from the brain area or structure you searched on. Tomorrow we’ll take a look at what the NIF Literature tab provides.

Other related blog posts:

NIF: When You’re Looking for Neuroscience Resources Including Data