Nervous System Connectivity Tutorial

Browse Nervous System Connectivity in NIF
For more information, visit the NeuroLex entry for Nervous System Connectivity

The NSC (Nervous System Connectivity) is not a single database; rather it is a view that includes data from 4 major connectivity databases including BAMS, CoCoMac, ConnectomeWIKI, and temporal-lobe.com.  The data is based on published work from various species, noted in the species column. All four sources focus on different brain regions and species. 

BAMS, The Brain Architecture Management System is a searchable atlas and structure hierarchy where a set of authoritative data resides on brain connectivity in addition to brain parts and cell types.

Most annotations are based on various atlases created by Dr. Swanson and colleagues, but BAMS lists data from other atlases. Note if the same structure appears several times as a result in NIF, this may be the reason. If the structure was labeled in 4 atlases then there will be four entries, one for each atlas.

For up to date issues or problems with BAMS, please see the wiki.

CoCoMac (Collations of Connectivity data on the Macaque brain) is a systematic record of the known wiring of the primate brain. The main database contains details of hundreds of tracing studies and their original descriptions.  This is a rich source of data for monkey, mostly Macaque brain connectivity.

For up to date issues or problems with CoCoMac, please see the wiki.

ConnectomeWIKI is a knowledge base for macro- and mesoscale brain region and brain connectivity information across species.  It is built using modern semantic wiki technology, meaning that it is a resource added to and maintained by a community of users.

For up to date issues or problems with ConnectomeWIKI, please see the wiki.

Temporal-lobe.com provides a hippocampal parahippocampal table that offers a display of known connections of the rat parahippocampal-hippocampal region of rat, published online and in paper form by Natalie Cappaert and Niels van Strien. The table, together with the references, provides a fully searchable knowledgebase of hippocampal-parahippocampal connections in the rat.  However, the full complexity of the temporal lobe resource could not be brought into the NIF system, so going to the temporal lobe site is the only way to search for subregions of the hippocampus

For up to date issues or problems with Temporal-lobe.com, please see the wiki.

The UCLA Multimodal Connectivity Database is a web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data. Anyone can browse and analyze connectivity matrices that researchers have shared on this site. The data comes from different imaging modalities, subject groups, and studies. The combination of easy data sharing and web-based analysis allows researchers to explore and compare brain connectivity datasets in a new way.

Webinar for The UCLA Multimodal Connectivity Database is available through NIF. Click the picture below to watch the webinar

 

To get to any of the data in this view, one can search for a brain region and look under Data Set > Connectivity 

The search for CA1 reveals the connectivity information shown below.  Note, each entry in the database column tells the user where the particular piece of data was obtained and where available the user can also click onto the blue link and be taken to the page in the database where the information is maintained.

Below are several example pages of what users will see when the follow the links to various databases.

Clicking on CoCoMac leads to the evidence pages for the connection, which can be difficult to read, but clicking on the source or target sites reveals the publications attached to each.  Evidence codes are also explained by clicking on each symbol, such as P.

Clicking on ConnectomeWIKI leads to the evidence page of this resource for the particular connection, here the CA1 to CA3.

Both BAMS and temporal-lobe.com links will lead to the front page of those resources where the user will have to navigate to the appropriate connectivity information.

In Temporal-lobe the connectivity information is maintained inside of a pdf file that need to be downloaded then it can be searched.