PubVenn: Visualize your PubMed searches

In my research career, I have searched PubMed A LOT. I thought I was doing pretty well at it too, although if I would have asked a librarian, I would have known what I was missing.

One of the most confusing parts about constructing searches is the boolean logic, more commonly known as the AND/OR/NOT part of the search strategy. Have you ever wished that PubMed would just draw you a picture your search? Well, now it can with PubVenn.

Ed Sperr, MLIS, created the PubVenn tool to visualize and refine search strategies using the bibliographic data and E-UTILITIES provided by NCBI. Librarians commonly use Venn Diagrams to think through their searches, but this tool automates this process (and probably catches some syntax errors in the process).

Let’s try an example. In my PhD work, I studied how a Toxoplasma gondii protein protects this parasite from being killed by macrophages during infection. So I’m going to search PubVenn for “(Toxoplasma gondii) AND macrophage”.toxoANDmacs

The left hand panel shows a Venn diagram of how these concepts overlap. The upper right hand panel shows the search PubMed performs* when you type in “Toxoplasma gondii AND macrophage”. I color coded it to match the colors in the diagram to illustrate which parts of the search correspond to which parts of the Venn diagram. The number of search results (1005) is also listed after the search strategy. It also lists the references in the right sidebar under the search strategy.

Additionally, you can explore the citations for each individual concept by clicking on the corresponding part of the Venn diagram, which causes the search strategy and the citation on the right to change accordingly.

So why is this important? Well, if I click on the macrophage circle and i’m seeing citations that I would like to see in my search, then I have to rethink my search strategy. Also, I’m a sucker for Venn diagrams.

*If you don’t know what the terms inside the brackets in this search strategy are doing, you can set up a consultation with a librarian or take one of our PubMed classes.