SumsDB Tutorial

For up to date issues or problems with this database please see the wiki.
For more information, please visit the Surface Management System Database.

SumsDB is a repository of many types of brain-mapping data.  One major data type, to which NIF is federated, is a set of ~40,000 stereotaxic coordinates (“foci”) reported in ~1,300 neuroimaging studies. This tutorial shows how to take a NIF search term and view the resulting stereotaxic coordinates in WebCaret, an online visualization tool for viewing SumsDB datasets.  Terms that work well for searching neuroimaging studies include topics related to function (e.g., “attention” or “motion”), disease (e.g., “autism”), brain regions (e.g., pulvinar”) and cortical areas (e.g., “area 21”).

Begin by entering a search term of interest.  For this example we will use "Autism".

Under the Data Federation tab, select Brain Activation Foci and then SumsDB.  The table shows some core information from the studies that include data on the topic of Autism.  There are hundreds of search results shown one page at a time (e.g., page 3 in this example).  The first column is the study name.  This is linked to a page in SumsDB that shows the study specific information (title, authors, citation, abstract, links to the article itself, the stereotaxic information, as well as where the activation foci were found within the article – tables, figures, pages and supplemental data).

The next column, Foci Description, provides a short descriptor of what that particular focus represents, as extracted from the study by a curator. The word autism is included in many of these descriptors. This is useful for quick reference.

The next three columns, X Y and Z, are the stereotaxic coordinates reported in the study. The Foci column lists the individual Foci ID numbers. This number is linked to a SumsDB page displaying the specific data for that individual focus. This information includes everything from the NIF table plus the size, statistic, distance above the surface, where in the study it was found, as well as the basic study information.



The final three columns include the Hemisphere of the brain, the Geography (or anatomical location) and the Brodmann area in which the focus was located.

To view these results on a human atlas surface, first click on “View in SumsDB” in the upper right hand corner.

This will take you to a table of the full list of results, found by NIF, in SumsDB.  From here, there are three options of how to choose foci to view.  Option 1 is to select the “Select All Pages” check box (located just left of center, below), which will select all foci from all pages available.  (Beware – if there are hundreds or thousands of foci, this may take a minute or two.)  Option 2 is to select individual foci from each page by selecting their individual check boxes – if this is done, the “Save Selected to Buffer” button must be clicked before moving to another page.  Option 3 is to select an entire page by selecting the check box at the top of the far left column (as shown below). 

Once you make a selection, click the “View in WebCaret” button.  In the first popup box, select “Yes” to have Sums launch WebCaret.  In the next message box, keep the default settings to Append to currently loaded foci (since there are none loaded yet, this is not a problem) and click the “Submit” button.  Wait for the popup that says the foci have been successfully loaded and click the “Close Window” button.  Then go to the Display Control Dialog and select “Show Foci”, the following image will appear.

The 3D coordinates are displayed as colored spheres on a human atlas surface.  The foci are all colored according to the study they belong to.  Click the Display Color Key button at the bottom of the Display Control to see what color represents which study.  You can then click on any of the color bars to enlarge the foci from that study.

Each focus is linked with its individual information.  By clicking on a particular focus, the information will come up in an Identify Window.  This information includes the focus specific data, the study information, along with links to the article itself (DOI/URL) and the PubMed link.

Foci from both left and right hemispheres are displayed on the default right atlas hemisphere.  To view the foci on the correct hemisphere, first select the “Preserve Foci, Foci Colors, and Study Metadata When Changing Scenes” check box in the Display Control.  In the main window, select the pull down Scenes menu and select the second option, “PALS Inflated (Both hemispheres), quick-load.”

This will open a second viewing window displaying the right hemisphere with the left hemisphere now displayed in the main window.  Select the “Show Foci on Correct Hemisphere Only” check box in the Display Control.  This is useful to view symmetries and asymmetries in the data, between hemispheres.

For further searching capabilities please visit SumsDB.