PubGene is breaking down the barriers that make understanding genetic research so difficult

John Erik Stacy 14 Dec 2007

PubGene, a company with its roots in research at the Norwegian Cancer Hospital in Oslo, is a pioneer and world leader in presenting genetics information. PubGene has built systems to search electronically stored biomedical literature and extract information relevant to genetics. Researchers can thereby quickly focus a search to their material of interest. But not only does PubGene provide a quick way to find genetics relevant info, it also finds relevant connections between genes. Although the internet is replete with sources of information, complex topics such as genetics “live” as long lists making it very difficult to get an initial overview. PubGene presents information as graphic images. So, for example, if you are interested in genes related to obesity, you can perform a search and the genes most commonly associated with the term appear in network around the term (see figure). By showing the way to connections PubGene helps to speed the discovery process in genetics research.

Cutting through jargon

The company also takes into account the issue of jargon. If you type the word “genome” Word for Windows will suggest that perhaps you meant “gnome”. This little example shows that – even though gene talk has penetrated into the popular press and CSI on TV – we have only the vaguest ideas of what the talk is all about. Researchers working in the field are, of course, much more comfortable with the jargon. But even experts can end up talking “past” one another. This is in part because some genes have many names and sometimes unrelated genes share a “nick-name”. Although there are international standards, nick-names die hard. PubGene has developed systems to resolve many of these naming issues and recognize alternate names for genes and concepts.

PubGene is now working to apply its technologies to other domains in the health sciences and beyond. The challenge is to find ways to allow users to view information at an appropriate level of complexity. A guiding principal is that users should be able to navigate through layers of cross-referenced information presented in graphical overview and “drill down” where specifics are necessary. The business model at PubGene includes contracting projects to pharma and its systems are honed through use at its public service internet site. To learn more about how PubGene works and the people behind it, visit www.pubgene.com.

This article was also published in the Dec 14th 2007 issue of the Norwegian American Weekly. For more information about the Norwegian American Weekly or to subscribe, call us toll free (800) 305-0217 or email subscribe@norway.com.