GoPubMed – PubMed browsing using ontologies

By Grant Jacobs 01/09/2010

A brief look at GoPubMed, an ontology-based browser for PubMed. (Intended for those who use the biological research literature.)

While reading an article at Nature Network, a commenter (David Crotty) pointed to GoPubMed, a service I have heard of but not tried before, built on a commercial knowledge-base server. This short post is to introduce this to my readers, and hear your thoughts on it. (Plug them in the comment box below this article.)

Basically, GOPubMed is PubMed sorted using the GO and MeSH ontologies (explained below) so that you browse the contents based on these ontologies, rather than just rely on search strings.

GoPubMed is mostly self-explanatory: I suggest people just wander over and try it out. Nevertheless, I’ve jotted down a few tips from my few minutes of exploration, for whatever they’re worth.


First, what’s an ontology? it’s a hierarchal collection of terms describing a domain of knowledge (biology, medicine, whatever). The ontologies GoPubMed uses should already be familiar to most biologists. GO is Gene Ontology and MeSH the Medical Subject Headings, a vocabulary thesaurus from the National Library of Medicine (USA). MeSH is now 50 years old! GO terms are shown with blue icons, MeSH terms using green icons.


To the left of the page is a familiarly-styled list of items, initially displaying from all of the contents in PubMed. Clicking on the arrows to the left will cause the topics to be expanded as you’d expect. If you’re looking for a very popular topic, you could just browse that way, although you’ll run into the usual problem on PubMed of there being just too much to read!

If you enter a search string (textbox in main pane), it’ll give you a description if it is able t0 (so if you give a gene name, you’ll get a brief description of the gene). Pressing on ‘search’ to the right of the textbox will update the browser to the left, so that it’s hierarchy is restricted by that term.

If you click on a subtopic itself, you’ll be presented with a floating menubar of options: Actions (with, without, and favourites; see below), Description (a short description of the ontology term), Tree (the part of the ontology tree the term falls within), and Wikipedia (a link to the Wikipedia entry for the term selected). You’ll sometimes also get synonyms where appropriate.

Actions are self-explanatory: they allow to add the term to your query (with), exclude it (without) or add it to your favourites. You’ll see as you add things, that the search string gets updated and new items appear in ‘my search’ section (top, left).


Results can be exported in RDF, EndNote, BibTex (Yay!) and text formats. (Nice to see the latter too: useful for those handy with programming tools and as a fall-back.) You’re limited to exporting 100 results at a time. To export, press ‘find it’ to bring up your results, then click on the icon with the arrow pointing to a computer (shown to right). Exports go straight to ’standard’ filename on some browsers, something I don’t like.


The service is English-only at present.

If you are using the clipboard (to the left, top), bear in mind it’s contents only last as long as your current session: save anything you want before you move on to the next thing!

If you know them, you can use the Search Field Descriptions and Tags from PubMed.

To the top you will see links to other services I haven’t looked at here: Go3R, GoGene, and GoWeb. GoWeb is like GoPubMed, but searches the internet. Go3R apparently provides alternatives to animal experiments. GoGene, as you might expect, searches gene annotation.

Other articles at Code for life:

Preserving endangered species – of gut microbes

Who blogs on what, and why

The roots of bioinformatics

What is your relationship with your research notebook?

Professors, lost souls with great oratory power?

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