A new website, Diseasome, visualizes 516 diseases and 903 genes to show common backgrounds and effects. The result is an interactive map showing how groups of diseases, say Cancer, share a common background and genetic material but manifest in slightly different ways. There is also a wealth of information about how they did it:
Nodes are positioned on the map according to a topological placement algorithm, i.e. each node is positioned solely according to its linking pattern. Many softwares are available for doing this. Gephi has been chosen for its high quality algorithm ForceAtlas.
Many algorithms make possible for a 2D rendering of an adjacent matrix – i.e. the matrix describing any graph. We used a ForceAtlas algorithm, which shares with all the others the same basic principle: minimizing the system’s energy while maximizing the use of the space available for the representation of the data. To minimize the system’s energy, one can for instance assume that nodes that are not linked to each other are pushing away from each other whereas nodes that are linked to each other are attracting each other. Through iterative steps the algorithm tries to find a way to position nodes where there is as little link overlap as possible. To maximize the use of the mapped space, the graph is spread as much as possible over the surface allocated for its display.
You can view the map at their site, http://diseasome.eu/, as well as buy a Poster or the Book.
Data from the same study is also visualized here: http://www.nytimes.com/interactive/2008/05/05/science/20080506_DISEASE.html
Even the simple visualization provided by the New York Times works pretty well and provides better context for the enlarged area. I wish the Fisheye would work better in the Gephi version.