new classification/modeling for infectious diseases Part 2

[nicolevasilevsky]

Now that we're nearly done with reclassifications of viral infectious disease (see #2950), we should apply this same modeling to bacteria and maybe fungus and parasites too.

Let's work on this together after the ICBO paper is submitted.

Here are our figures for our reference:

Yellow = new terms we added
Blue = existing terms
Oval shape = terms overall in both figures

[nicolevasilevsky]

Addition things to do:

• review - when we should use that more general relation 'disease has infectious agent' vs when to use primary infection