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A more automated approach could be done with a plugin. For instance in my goodreads metadata download i put in place a hardcoded mapping between what values it could supply as tags and a smaller subset of tag names within calibre. A a more general approach across multiple metadata sources is an idea I have had for a while but it would require an extra step in your process as a plugin. ie hit ctrl d to get the tags then another keyboard shortcut or menu option to clean them up. The idea being that you would define in a similar way to goodreads but with a gui the mappings so all your sci fi variants go to a single Science Fiction tag for instance. Anything not defined in your list of mappings would get discarded.
A number of people disable tags because they are too random for their liking. His approach might give a better working subset. If it sounds of interest then post it in the plugin ideas thread.
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