Contents


Introduction to the Internet Brain Volume Database (IBVD)

http://www.cma.mgh.harvard.edu/ibvd

Goals

The goal of IBVD is to provide a web-based searchable database of brain neuroanatomic volumetric observations. This is designed to access both group volumetric results as well as volume observations in individual cases. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the disemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as metaanalysis. Extensions that permit pre-published, non-published and other representation are planned, again to facilitate comparitive analyses.

Principle Design Strategy

We have chosen to follow the following design strategy. The principle organizing data structure is the 'publication'. Publications report on 'groups' of subjects. These groups have 'demographic' information as well as 'volume' information for the group as a whole. Groups are comprised of 'individuals', which also have demographic and volume information for each of the individuals. The finest-grained data structure is the 'individual volume record' which contains a volume observation, the units for the observation, and a pointer to the demographic record for individual upon which the observation is derived. A collection of individual volumes can be groupd into a 'group volume' observation; the group can be demographically characterized by the distribution of individual demographic observations for the members of the group.

Walk Through/Tutorial

To get the essence of the site, the following set of instructions provide an annotated sampling of the existing functionallity.
  1. Point browser to http://www.cma.mgh.harvard.edu/ibvd. This brings up the main page, from which all subsequent actions can be accessed.
  2. Click on 'display (display single elements, including publication)' This brings up an interface to the database records.
  3. Click on 'Submit Query' on the Publication line (leave the entry field as 'all') This generates a one-line listing of all publications index in the database, including the 'pub ID' by which each of the publications are indexed.
  4. Click on a sample pub ID (such as 'pub ID 65') This shows the complete publication record, including reference out to PUBMED, as well as the groups and individuals reported in this publication, and any groups citing this publication as their method.
  5. Click on a sample group demographic record (such as 'grp dem ID 44') This shows the demographic information for the group, as well as all group volumes reported for this group.
  6. Click on a sample grp vol id (such as 839) This shows the group volume record.
  7. The above steps review each of the elements of data encoding. We next look at the search structures that are enables. At the top of the page, click on the 'search (search for volumes)' link. This brings you to the main search generation page.
  8. Formulate a sample search query (such as select 'Brain' from the structure list, 'Normal' from the diagnosis list, and deselect all options except 'total' from the hemisphere check boxs). Then scroll down to select 'Submit Query'. This brings you to the results of the search. This page reviews the search criteria, declares how many matches were found, gives you the option to save the results into a text file, gives you the option to plot the results (volume as a functions of age), and displays the complete set of matching records for the search.
  9. To simply review the results of the search, select 'plot volume'. This generates a simple plot of the volumes reported as a function of age.
  10. To make the plot somewhat more interesting, send your browser back one page, and in the plot options portion of this page, select 'diagnosis' for the use plot color to flag, and select the check boxs for both 'show age error bars' and 'show volume error bars'. Hit 'plot volume' again. The resultant plot now includes error bars on both the age and volume axes. Since the search was only conducted for diagnosis 'Normal', only normal is plotted and annotated.
  11. Now, try other more interesting searches and plots to get a feel for the database contents. The most obvious is to repeat the brain volume search you just did, but do not select for Normal, select for all (select none in the diagnosis list). The resulting plot is much more interesting!
  12. Have fun!