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What cataloguing system are you using?
In Calibre, my ebooks are tagged by subgenre which form the basis of the shelves on my Kobo. These tags are replicated along with many more in my LibraryThing account, which has genre-based collections. I have some condition tags - Needs cover, Replace for scanned
In general, sub-genre tags will only appear in a single genre collection. These tags are then supplemented by descriptive tags: historical fiction (general, crime or fantasy) will get a time-period tag, or a geographic tag. Other tags I use are game system and setting for RPGs, I also need to tag rules and adventures. I don't bother with other tags in Calibre as tags aren't searchable on the Kobo.
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