SumsDB Tutorial

Browse SumsDB data in NIF
For more information, visit SumsDB or the NeuroLex entry  for SumsDB

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 Nervous System Function 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. (You can choose to see 10, 25 or 50 results at a time in the table. This will come into play a little later.) 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 WebCaret from SumsDB displaying the focus. At times it is not possible to see a focus on the brain, which means that the focus is deep in the brain and can often be found if the user manipulates the brain (more on this below).

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.

You can view these foci results as spheres on a human atlas surface. Here is where the “Page size” comes into play. However many you have chosen to view in the table is how many will show on the atlas surface. (In the example below 50 foci will appear on the atlas surface.) Once you decide how many to view, and from which page of results, click on the “View on Brain” link in the upper right hand corner of the table.

After clicking the “View on Brain” link you will see the following window appear, showing the selected page of foci. The foci are colored by the study they were reported in.  To find out which color represents which study, click on the D/C button in the WebCaret toolbar.

Change the Page Selection to Foci and click the Display Color Key button at the bottom of the page 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.

You can also view foci on an atlas surface by choosing the View in SumsDB.

This will take you to the page worth of results, listed in the NIF table, in SumsDB. From here, there are two options of how to choose foci to view. Option 1 is to individual foci from the list by selecting their individual check boxes. Option 2 is to select the 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 “Quick View in WebCaret” button. The next steps will be the same as above.

Or you can 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”. Then you can proceed as above.