I'm looking for a free software tool, R-package or Matlab script to create interactive 3D scatter plots of biological data (gene and protein expression data, or metabolite abundances), which allows the users to add biological annotations to the data points (representing biomolecules) and display them when a user hovers the mouse over them. I found many scatter plot tools so far, but adding interactive annotations does not seem to be supported in most cases.

Many thanks for your help.
You can try the R-package [vrmlgen][1] which provides annotated 3D scatter plots in VRML and LiveGraphics3D format (see also page 7 of the [documentation][2]). Works also with large numbers of data points.

 [1]: http://cran.r-project.org/web/packages/vrmlgen/index.html
 [2]: http://www.jstatsoft.org/v36/i08/paper