Here's a discussion on the principles and practice of building a thesaurus:

http://www.willpowerinfo.co.uk/thesprin.htm

This should give you the kind of guidance you need.

Sounds like you already have the software, but if not, there are discussions of available software at the links below:

http://www.willpowerinfo.co.uk/thessoft.htm

http://www.asindexing.org/site/thessoft.shtml

http://www.termtree.com.au/

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