Program Session

12 - Visualizing PubMed: Displaying Search Results by Topic, Region, and Time

Tuesday, May 30
4:00 PM - 4:05 PM
Room: 611

Objectives: This project is an attempt to visualize the results of PubMed searches in a variety of different ways: topics and how they overlap with Venn diagrams, aspects of a search (MeSH categories and subheadings) with bar graphs, geographic areas by choropleth, and how results change by year using a line graph.


Methods: Using the NCBI API (E-utilities), a series of tools have been developed to visualize PubMed searches. Querying of the API and parsing of the results is done in the browser via JavaScript/jQuery. Visualization of results is also done in the browser (for the most part with Google Charts and with the venn.js overlay of d3.js for Venn diagrams).

Results: The applications successfully display a visualization of the aggregate results of an individual search and facilitate the easy comparison of that search with others. The applications and their source code can be found at https://github.com/esperr.

Conclusion: Visualizing the results of a search in aggregate is a potentially useful way for experienced searchers to refine their search strategies. Viewing PubMed in this way is also an interesting exercise for those who utilize bibliometric analysis of the biomedical literature. Finally, these applications are intended as examples of how relatively simple programing can stitch together APIs and libraries to create new interfaces to our databases.

Keywords: PubMed,
data visualization,
bibliometrics,
database interfaces



Program Session

Edwin V. Sperr

Clinical Librarian
Augusta University/University of Georgia Medical Partnership
Athens, Georgia

Ed Sperr, M.L.I.S. has served the Augusta University/University of Georgia Medical Partnership since 2016, when he was hired as that institution's first Clinical Information Librarian. Ed provides point-of-care information to the Residents in the Graduate Medical Education program and works with them to develop the skills needed to find and evaluate the information necessary for clinical decision-making. A native of Augusta, Georgia, Ed has also worked in health science libraries in South Carolina, Massachusetts and the Caribbean. His current area of research is using visualization tools to explore bibliographic citations.

Presentation(s):

Send Email for Edwin Sperr


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12 - Visualizing PubMed: Displaying Search Results by Topic, Region, and Time

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