I am currently using MS Access for a risk management database and, through some visual basic magic, MS Visio is able to extract the data from this database and create a visual representation of the data. It is great for communication of this information.
I would like to use a OS X compatable product such as OmniGraffle Pro or ConceptDraw but there is almost zero information available out there on any ability to do this.
OmniGraffle is fantastic and has a great applescript library. Filemaker's applescript library is OK too. You should be able to write an Applescript that will do the whole thing. If OmniGraffle doesn't do what you want you could use Smile to draw objects from scratch.