I would also recommend TiddlyMap, but it may get a bit unwieldy if you have 
300 nodes. 

I doubt that anything will be finished in time to be very useful by monday, 
but I am hoping to make a generic encyclopedia model for TiddlyWiki using a 
lot of things I have made 
<http://ooktech.com/jed/ExampleWikis/Directory.html>. While it isn't 
immediately obvious a lot of the functionality you want is already in what 
I made. Unfortunately one of the biggest problems with TiddlyWiki at the 
moment is the difficultly going from understanding the very basic use as 
something like a journal or linked notebook to understanding more complex 
uses. We are working on it.

In the meantime, everything in your list (all the plants belonging to X 
family, listing all plants with medicinal "root bark", etc.) can be done 
relatively simply using what you inspired me to make from your request (here 
<https://dl.dropboxusercontent.com/s/2j4326k9mispk41/GenericFieldsAsTags.html?dl=0>).
 
I am working to find a reasonable way for someone who isn't familiar with 
TiddlyWiki to use them effectively.

Once I get the new changes added into the encyclopedia demo I made than 
just clicking on the tag pill for each section will list everything that 
has that entry. So everything that has antiseptic listed under uses will 
appear if you click on the pill antiseptic in the uses list.
There are other ways it will be able to be sorted or searched through as 
well, like a drop down menu where you can select from all the uses to get a 
list of things that match it.

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