Mining the neuroimaging literature using the SumsDB database: stereotaxic coordinates and more!
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1
Washington University School of Medicine, United States
A PubMed search reveals more than 50,000 studies related to functional imaging of the human brain. More than 10,000 of these studies report key experimental data (centers of fMRI activation foci, etc.) in tables of stereotaxic coordinates (‘foci’) in one or another standardized atlas space. To effectively mine the data underlying this extensive literature, a robust database infrastructure is sorely needed. To this end, we have developed the the SumsDB database (http://sumsdb.wustl.edu/sums/) that supports storage, visualization, and searching of many types of neuroimaging data. Recent advances include customized ‘libraries’ for handling stereotaxic coordinates (‘foci’ in our terminology). This demo will illustrate how to use the SumsDB ‘Quick-Search Repository’, which currently contains ~40,000 foci from ~1,300 published studies, including comprehensive coverage of four major journals. These foci can be viewed online using WebCaret and a population-average human atlas (Fig. 1A). Searches can be based on many criteria, including cortical area or region (‘area MT+’, Fig. 1B), spatial coordinates, functional criteria (‘music’, Fig. 1C), or disease condition. Search results can be viewed online (WebCaret) or downloaded for offline visualization and analysis using Caret sofware. SumsDB search results can also be obtained through data mining initiated using the Neuroscience Information Framework (NIF, http:// neuinfo.org/), a portal whose searches can be refined or expanded using the NIFSTD neuroscience ontology. We are enlisting volunteers to contribute data to the SumsDB Foci Library, so that it more quickly approaches comprehensive coverage of the literature.
SumsDB also includes publicly available surface and volume data from many published studies. Bi-directional links (between the online study and SumsDB and vice-versa) are coupled with WebCaret ‘scenes’ that recapitulate the layout of individual figure panels and provide an efficient starting point for mining the underlying datasets. As the amount of such data incorporated into SumsDB continues to grow, this will enable cross-study comparisons as well as formal meta-analyses that capitalize on the greater richness and spatial complexity of volume and surface datasets compared to stereotaxic coordinates.
Conference:
Neuroinformatics 2009, Pilsen, Czechia, 6 Sep - 8 Sep, 2009.
Presentation Type:
Oral Presentation
Topic:
Neuroimaging
Citation:
Van Essen
D,
Reid
E,
Gu
P and
Harwell
J
(2019). Mining the neuroimaging literature using the SumsDB database: stereotaxic coordinates and more!.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2009.
doi: 10.3389/conf.neuro.11.2009.08.021
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Received:
21 May 2009;
Published Online:
09 May 2019.
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Correspondence:
David Van Essen, Washington University School of Medicine, St Louis, United States, vanessen@brainvis.wustl.edu